Over the past few decades, Iran has seen a revival in the native religion that predates Islam—something that the ayatollahs desperately want to suppress.

Ask someone about the Zoroastrian religion and—assuming they’ve heard of it—you will typically get three responses. Your interlocutor might inaccurately describe followers of the Zoroastrian faith as “fire-worshippers.” He or she may recognize Zoroaster, the priest who founded the religion, as the protagonist of the German philosopher Friedrich Nietzsche’s classic work, “Thus Spoke Zarathustra.” And there’s the oft-quoted “fun fact” that Freddie Mercury, the flamboyant vocalist of rock group Queen, was and still is the world’s most famous Zoroastrian.

Much less well-known is that Zoroastrianism is a living faith, with communities in India, Europe, the United States, and the Middle East—especially Iran. Ten years ago, a study by the Federation of Zoroastrian Associations of America concluded that there were, at most, 190,000 followers of the faith around the world. But as Laurie Goodstein noted in The New York Times, there was reason to be skeptical of this number, because of the “wildly diverging counts in Iran, once known as Persia – the incubator of the faith.”

In common with other religions, Zoroastrians in Iran have confronted both persecution and a concerted attempt by the Islamist regime in Tehran to destroy the very foundations of their faith. One critical consequence of this—no doubt unintended by the ruling mullahs—is that growing numbers of Iranians inside and outside the country are exploring a faith that crystallized two millennia before the Prophet Muhammed appeared on the scene. “Converting back” to Zoroastrianism, as many refer to the process of rediscovering their roots, has encouraged a view of Islam as an alien Arab faith that was imposed on unwilling Persians during the Muslim conquest of the seventh century.

For most of his childhood in pre-revolutionary Iran, Dr. Ali M. heard virtually nothing about his family’s religious heritage. (He declined to share his full name out of concern for family members still living in the country) But when Ayatollah Ruhollah Khomeini seized power following the 1979 revolution that overthrew the Shah, Ali’s family left for Germany. Experiencing a foreign culture for the first time, Ali, who now works as a physician in southern California, began to ask questions about his background. “When I lived in Germany, I was going through my teenage years,” he explained. “I tried to find out who I am and what was going on around me in a world of chaos and displacement.”

Ali began asking his parents about their religious heritage and ancient roots. That’s when he found out through conversations with his mother that his grandfather’s family was descended from the Zoroastrian priestly lineage.

Anxious to acquire more knowledge about his hidden faith, Ali began studying Zoroastrian teachings. He learned about the three principles propagated by Zoroaster: Humata, Hukhta, and Hvarshta, “Good Thoughts, Good Words, and Good Deeds” in Avestan, an ancient Iranian language. He learned that fire, which plays such a central role in Zoroastrian religious ceremonies, represents the divine light of wisdom. Then he decided to undergo the Navjote, an initiation ceremony into the faith that is similar to a Bar Mitzvah.

At first, the priests whom Ali met in America were apprehensive about performing the ceremony, pointing out that doing so would be regarded as apostasy by Iran’s rulers, which could cost Ali his life if he returned home. According to Iran’s official records, Ali’s father is registered as a Muslim. Under Iranian law, children automatically take their father’s religion. Iranians who depart Islam for another faith face imprisonment or even execution.

Ali was devastated and angry. “I was in tears, I was actually crying,” he said. “I said I don’t need these people to prove who I am. I was going to find somebody to do this for me, so I could formally declare my belief.” Eventually he found a Zoroastrian priest to perform his Navjote.

“I felt that I’m the same person and have always been a Zoroastrian,” Ali said, reflecting on the experience. “Even though I grew up in a household where religion didn’t play a central role and was never forced on me.” Ali now believes in asha, a Zoroastrian concept meaning “the path of truth and righteousness”—that things always fall into place if you follow the right path.

In the seventh century, Arab tribes armed with the Quran patched together the former territories of the Sassanian Empire, the last pre-Islamic Persian dynasty, forcing the conquered population to adopt Islam. As a result, some Zoroastrians fled Iran for lands as varied as China, India, and the Balkans. But many stayed behind, resisting the Arabs for 200 years, in what some call “The First Arab Occupation.”

“Students were taught that Zoroastrian priests and the Sassanians were barbarians, and that the Arabs had to come in to ‘civilize the people,’” said Dinyar, a Zoroastrian historian asked to use a pseudonym because he regularly travels to Iran.

Zoroastrians continued to resist conversion despite continued persecution. By the 15th century, a sizeable portion of Persia’s population still remained Zoroastrian, especially in the northern provinces of Gilan and Mazandaran. Their continuing presence raised concerns among the Muslim clergy that others might probe their roots and family backgrounds and leave Islam.

“Those who did not convert had to pay jizya, the infidel tax,” explained Dr. Daryoush Jahanian, a leading Zoroastrian scholar. “If they could not afford the tax, they were subjected to torture, confiscation of property, and even threats to their life.” Another humiliation imposed on the Zoroastrians, along with other religious minorities, was a law compelling them to wear a yellow patch on their clothing to mark them out —a badge of inferiority that the Jews of Europe were all too familiar with. Many Zoroastrians were shepherded into ghettoes known as gavrestan. “In Persian, that word is reminiscent of ‘goorestan’ or cemetery,” Dr. Jahanian added. “In this hostile environment Zoroastrians were even blamed for natural disasters such as earthquakes and floods.”

Iranian scholars point to 1979 as the year that reignited the innate curiosity of many Iranians regarding their roots and origin. After the revolution, Iran became estranged from the Shah’s Western allies, forcing ordinary Iranians to examine their national and spiritual identities.

The revolution dislodged the Pahlavi dynasty, founded by Reza Shah Pahlavi in 1925, who was then succeeded by his son, Mohammad Reza Shah Pahlavi. The Pahlavis combined brutal authoritarianism with secularism and an embrace of Western norms and customs. For the Zoroastrians, this meant recognition of their faith and even the official adoption of some of their traditions, like Nowruz, the Iranian New Year, and the celebration of the spring equinox.

In the early 1970s, the Shah encouraged the return of Parsis, Zoroastrians who had been living in India for centuries. Iranian Prime Minister Asadollah Alam met with several Parsi businessmen who were urged to invest in Iran. Many Parsis did just that, including a significant number who relocated to Iran.

“In the 1970s, ancient Iranian stuff was really in and cool,” Ali recalled. “People wanted to connect to that—especially educated people, who thought Islam was more of a regressive factor in Iranian culture. That’s still a very strongly held belief, especially among the younger generation, hence the animosity and misplaced anger toward Arabs and Arab culture.

“When I was growing up in Iran, and somebody was wearing a chador, a full body covering worn over regular clothes by women, or even a headscarf, they were either thought to be a maid, a peasant, or somebody who’s very uneducated,” he added. “And that association kind of remained.”

Once Khomeini was in power, the tentative revival of Zoroastrianism in Iran was suddenly halted, and Zoroastrians started to flee the country. In the main Zoroastrian temple in Tehran, the portrait of Zoroaster was replaced with a portrait of Khomeini. As far as Khomeini was concerned, Zoroastrians were, as he wrote before the revolution, “dishonorable, fire-worshipping knaves…if this fire of dirt that has risen from the temples of Fars is not extinguished, soon the trash will spread and they invite all to join the [Zoroastrian] creed.”

As Dr. Jahanian pointed out, scholars of Zoroastrian and ancient Iranian studies were persecuted after 1979. “Many suffered physical, psychological, and financial punishments,” Jahanian said. “Some were arrested, jailed, and beaten. Others lost their jobs and even suffered the loss of a dear one.”

Furthermore, Zoroastrians, including other religious minorities, were by law prohibited from holding senior government or military positions. They were also discriminated against in the legal system, receiving more severe punishments and worse lawsuit settlements than Muslims do. Today, Zoroastrians—officially numbered, according to Iran’s 2011 census, at just over 25,000—are still subjected to apartheid-like legislation: No more than 3,000 copies of any religious text may be printed, and principals of Zoroastrian schools must be Muslims.

Even so, many Zoroastrians have clung stubbornly to their beliefs and practices, even performing conversions in private. Those who fled abroad experienced a similar awakening. “I felt that I had found my identity,” said Shahrooz Ash, born in Tehran to secular Muslim parents who emigrated to England. “I felt I had returned home to who I really was, to my roots. A lifelong search of who I was and where I came from had finally reached its destination.”

Ash has not returned to Iran since the revolution. After his time in England, he came to America, where he studied philosophy at UCLA. An encounter with a philosophy professor, who asked him about pre-Islamic Iran, a subject about which he knew almost nothing, spurred him on to further study. “I was ashamed that I did not know my own roots, the glorious and powerful ancient people I came from,” he said.

Ash said that his true identity, like many Iranians, had been overwhelmed by the impact of the Islamist revolution. “Iranians are,” he said, “conflicted between these two identities, between being Iranian and being Muslim.”

Dr. Jahanian describes the arrival of the internet as a “miracle” because of its role in the Zoroastrian awakening—just one of myriad reasons why the Iranian regime exercises such strict control over its own sphere of cyberspace.

Among the leaders of this information revolution is Dr. Shahin Nezhad, an academic who specializes in ancient Iran. Nezhad and a group of scholars and cultural activists are the founders of the Persian Renaissance Foundation, the main backer of the Iranian Renaissance Movement, which produces content aimed specifically at audiences in Iran.

Nezhad, now 48, was born to non-practicing Muslim parents in Iran. “My parents were not Muslim by belief or by practice, but since I was not in any other category, I was recognized as Muslim. This is the case for millions of Iranians,” he said.

Nezhad pursued a career in petroleum engineering and transferred to Houston to work for an oil company. He had always been interested in history, politics, and his ancient Zoroastrian roots.

“I had a very strong tendency to Zoroastrianism as a philosophy, as a national heritage, and that’s the tendency among many, many Iranians,” he said. “So they look at the Zoroastrian culture and religion as something that really belongs to their ancient, Persian heritage or old Iran.”

Nezhad started to consider himself a Zoroastrian in his early twenties, and began following the Gathas, the most sacred Zoroastrian texts, consisting of 17 hymns composed by Zoroaster. They are essentially a philosophy on how to create a balanced and peaceful life.

Nezhad eventually decided to perform his Navjote in his early 40s—one day after marrying his wife, who is a Zoroastrian herself. However, Nezhad always felt that in his heart he was Zoroastrian, and so didn’t need a formal conversion to tell him so. “For Iranians, you feel that being Zoroastrian is like being Iranian,” he said. “Being Muslim is not really being Iranian. It is a kind of an identity crisis for them. It’s very complicated.”

Nezhad foresees “an Iranian Iran” with a significant Zoroastrian population, which, he believes, will pacify the region, reducing tensions between the other nations and people.

“There is no state where Zoroastrians feel at home,” he argued. “Iran has to be their state, their stronghold, their center of attention and interest. And perhaps Iran can be the defender of the rights of Zoroastrians all around the world.”

Nezhad believes that a cultural revolution from within will gradually degrade the foundation of the current Islamist system of government. “Rather than going 180 degrees and opposing the establishment, we try to oppose them by awakening people to their real heritage and real identity, rather than what they are told by the current system,” he said. “Therefore, for time being, at least until we figure out something else, our strategy is education, education, education.”

The determination of Iranians to use the very online tools that the regime has actively tried to close down is a powerful signal that this learning process is finally underway. Scholars like Jahanian and Nezhad say that outside of the official figures, there are around 100,000 Zoroastrians who are formally registered as Muslims but practice Zoroastrianism. This, they say, is the cusp of a broader awareness among Iranians that their pre-Islamic past provides the grounding for a post-Islamist future in which all religions will coexist in equality.