"Death to Palestine" was spray painted on the Tayba Islamic Center on Coney Island Avenue in the Homecrest section.
The vandalism was found around 6 a.m., as Muslims celebrate Eid al-Fitr, the "Festival of Breaking the Fast," to mark the final day of Ramadan.
"We mark the end of Ramadan, we rejoice with our families, we start the morning with the prayer," worshipper Imran Khan said. "And I come in, 6 o'clock in the morning, to see that."
The congregation is mostly Pakistani-American, not Palestinian, but the impact is no less painful. Worshippers believe the motive is obvious.
"Even though the issues are 6,000 miles away, the hate is here," worshipper Mehran Mohammad said. "And it's festering."
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As the fighting rages in Israel and the Palestinian territories, tensions are rising across the globe -- and in New York, where supporters of the Palestinian cause have taken to the streets in large numbers.
Overall, hate crimes in New York City are up 71%, driven largely by anti-Asian bias crimes, which are up a staggering 376%. Anti-Black crimes are up 70% but anti-Semitic crimes are down 7% and anti-Muslim crimes are unchanged.
The community is diverse, a vibrant corner of South Brooklyn where Jews and Muslims live side by side. In fact, a yeshiva is just across the street from the mosque.
No one was more surprised than the Imam.
"I'm surprised when I saw this on the wall," Imam Mohammad Younas said. "And, hopefully, the NYPD get the person, whoever did this."
Police were hoping surveillance video will help lead to an arrest.
"We urge local, state and federal law enforcement authorities to investigate the apparent bias motive for this vandalism and call on elected leaders to denounce this hateful act and the violent rhetoric," CAIR-NY Legal Director Ahmed Mohamed said. "The Muslim community is facing attacks around the world, and the lack of effective responses to atrocities committed abroad seem to have emboldened those here to act on their hatred for Muslims and Palestinians."
The Hate Crimes Task Force is investigating, and anyone with information in regard to this incident is asked to call the NYPD's Crime Stoppers Hotline at 1-800-577-TIPS (8477) or for Spanish, 1-888-57-PISTA (74782).
The crime comes amid increasing violence between Israelis and Palestinians in the Middle East, with the region on edge amid a relentless escalation of hostilities -- even as Egyptian negotiators held in-person talks with the two sides, intensifying efforts at mediation.
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Previous fighting between Israel and Gaza's Hamas rulers, including a devastating 2014 war, was largely confined to the impoverished and blockaded Palestinian territory and Israeli communities on the frontier. But this round seems to be rippling farther and wider than at any time since the 2000 Palestinian intifada, or uprising.
While some rocket attacks have reached the Tel Aviv area, Arab and Jewish mobs have rampaged through the streets, savagely beating people and torching cars. Flights have been canceled or diverted away from the country's main airport.
Weary Palestinians, meanwhile, somberly marked the end of the Muslim holy month of Ramadan on Thursday as militants fired one barrage of rockets after another and Israel carried out waves of bone-rattling airstrikes. Since the rockets began Monday, Israel has toppled three high-rise buildings that it said housed Hamas facilities after warning civilians to evacuate.
(The Associated Press contributed to this report)
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