After the conference concluded, Ms. Afridi drove to the former concentration camp in Dachau, Germany. As she stood before the dun bricks of a crematorium, she prayed. “Inna lillahi wa inna ilayhi raji’un,” she said in Arabic, meaning, “Surely we belong to God and to him shall we return.”

“I didn’t know that moment would be defining my role,” Dr. Afridi, 44, said a few weeks ago. “I didn’t even realize then that I was at a crossroads. People see the Holocaust and Islam as two separate things, but these stories of faith and catastrophe are not opposites. They are companions.”

Dr. Afridi has made these seeming irreconcilables into companions in her life’s work. An assistant professor of religion at Manhattan College, she teaches courses about both Islam and the Holocaust, and she is director of the college’s Holocaust, Genocide and Interfaith Education Center. Her book “Shoah Through Muslim Eyes,” referring to an alternative term for the Holocaust, will be published in July, and she is a member of the ethics and religion committee of the United States Holocaust Memorial Museum in Washington.

Such roles have made Dr. Afridi both a valued intermediary and a visible target in the troubled relations between Muslims and Jews. As her research unflinchingly shows, a strain of Holocaust denial runs deep in the Arab-Muslim world. Holocaust recognition among Arabs and Muslims, less noticed but equally divisive, has also served as a means of delegitimizing Israel and Zionism. By this line of reasoning, which ignores the historical ties of Jews to Israel, the Holocaust was a crime inflicted by Europeans for which Palestinians paid the price.

While Dr. Afridi is an observant Muslim, praying daily and fasting during Ramadan, she is seen by Muslim critics as disloyal or naïve for putting her scholarly work at least partly in the service of chronicling a Jewish tragedy, rather than the defeat and dispossession that Palestinians call the Nakba. Moreover, she has studied in Israel and expressed support in her writings for a two-state solution for Israelis and Palestinians.

 “When I think about Mehnaz Afridi, I go back to the first generation of Christians who really engaged with the Holocaust, when the feelings were so fresh and deeply wounded,” said Michael Berenbaum, a prominent Holocaust historian who has been a mentor to Dr. Afridi. “Now there’s an even deeper, double-edged wound of Jews and Muslims seeing themselves as victims of the other. You only have two ultimate protections in the field: the quality of your scholarship and your ability to take a punch.”

Dr. Afridi’s resilience received a thorough field test after she joined Manhattan College in 2011. With her appointment, the college — a Catholic institution in the Bronx — expanded the mandate of its Holocaust center to cover other genocides, including those in Armenia and Cambodia.

“Six million dead Jews are weeping and screaming from their graves,” the blogger Pamela Geller wrote at the time. “And the Islamic supremacists are howling and rubbing their hooves together in anticipation. Such stupidity is without equal.”

Dov Hikind, a state assemblyman from a heavily Orthodox Jewish section of Brooklyn, told The Jewish Week of New York at the time that “the addition of Dr. Afridi and the expansion of the center’s mission diminish the magnitude of the Holocaust as a defining Jewish event.”

In the subsequent months, Dr. Afridi said, some Muslims called her a “Jew lover.” More troubling to her are the persistent rumors in Muslim circles that her scholarly work is being secretly funded by Jews.

Raked by those hostile crosswinds, Dr. Afridi keeps her address and the names of her family members confidential. Nothing, however, had led to self-censorship in her role as a public intellectual, she said.

“I have the empirical, existential understanding of my subject matter,” she said. “And I have the belief that if you speak for another, it means more than if you speak for yourself, for your own people. And when there’s so much daily tension between Muslims and Jews, it’s momentous for us to do this work, whether it’s me with the Shoah, or it’s a Jewish scholar speaking out about the Muslims in Bosnia or about Palestinian suffering. We are commanded by God to speak the truth.”

However divinely directed, Dr. Afridi had to make her own, idiosyncratic way. The child of a relatively secular banker and his more religious wife, she was raised in Pakistan, Dubai in the United Arab Emirates, England and Switzerland before coming to the United States in 1984 for her last two years of high school. She attended a school in Scarsdale, a suburb of New York with a large Jewish population. She was one of few Muslims in the area, and her introduction to interfaith relations involved being roughed up by her soccer teammates and hearing her parents being insulted.

Nearly a decade later, while pursuing a master’s degree in religious studies at Syracuse University, she served as a teaching assistant to Alan L. Berger, a professor specializing in Holocaust literature. Sensing her curiosity, he urged her to visit Israel, and she spent five weeks there in 1995, ostensibly to study biblical archaeology.

Under that guise, she threaded her way through Jerusalem, Tel Aviv, Haifa and the Palestinian territories of the West Bank. The experience magnified her interest in both Islam and Judaism. Along one axis, she earned a doctorate in Islam and religious studies from the University of South Africa. Along the other, as a visiting professor of theological studies at Loyola Marymount University in Los Angeles from 2003 to 2005, she began recording oral histories of Holocaust survivors.

 “At the end of the interviews, I’d explain that I’m Muslim,” she recalled, “and one woman said to me: ‘There’s Holocaust denial. What are you going to do about it?’ ”

Three months after that encounter, Dr. Afridi made her pilgrimage to Dachau, answering the survivor’s question by changing the direction of her academic career. Manhattan College’s search in 2011 for a professor who could teach about the Holocaust as well as Islam was almost providentially suited to her résumé.

For her course on “Religion and the Holocaust,” she faces one set of challenges — teaching about that terrible time in history to young people who often barely know it, and discussing Christian anti-Semitism’s role in the Shoah with students who are predominantly Christian. In her role as author, lecturer and director of a genocide center, she encounters Jews and Muslims, some supportive and others antagonistic, yet all, in her view, reachable.

“If a Muslim asks me why I’m not teaching about the Nakba, then I’ll say we already know about it, and what we need to learn about is the Holocaust,” she said. “And if a Jew tells me, ‘Muslims are Nazis,’ I’ll say, ‘Can we have lunch?’ These are the people we have to engage.”

The New York Times