The police said the imam, whom they identified as Maulama Akonjee, 55, and the assistant, Thara Uddin, 64, were shot shortly before 2 p.m. near the mosque, Al-Furqan Jame Masjid, in the Ozone Park neighborhood.
Officers found them with gunshot wounds to their heads when they arrived at the scene, at the corner Liberty Avenue and 79th Street. The police said that both men were taken to Jamaica Hospital Medical Center, where they died.
The crime, during a wave of anti-Muslim hostility across the country, unsettled many in the neighborhood, an enclave that area leaders described as a growing hub of Muslim families from Bangladesh that straddles the border between Brooklyn and Queens.
The two men had just left a prayer session at the mosque, according to Misba Abdin, 47, who attends the mosque and is a leader of an area nonprofit that works with Bangladeshi residents. Mr. Abdin and other congregants said that Mr. Akonjee, originally from Bangladesh, lived in the area.
The police said it appeared that Mr. Akonjee and Mr. Uddin were targeted but did not immediately release a motive for the shooting. They were wearing religious garb, and Mr. Akonjee was carrying more than $1,000, the police said. The money was not taken.
They were approached from behind by a man wearing a dark polo shirt and shorts as they were turning onto Liberty Avenue, according to witnesses and video footage from the area, the police said. Witnesses saw a man running away with a gun, the police said.
Police said that they were investigating what led to the shooting, saying they did not know whether it was related to a botched robbery, a dispute or anything tied to their religion or race. “There’s nothing in the preliminary investigation that would indicate that they were targeted by their faith,” said Henry Sautner, a deputy inspector in the New York Police Department.
A law enforcement official, speaking on the condition of anonymity because of the active investigation, said that the crime did not fit any existing pattern and cautioned that the motive was still wide open. “What it does seem is that it was planned, to some extent,” the official said.
Hundreds of Ozone Park residents rallied Saturday evening at the crime scene, a nondescript block underneath elevated subway tracks, to denounce the shooting. “We want justice!” they chanted over the sounds overhead of the subway and helicopters.
A few hours later, another group of residents, religious leaders and members of Muslim-American groups gathered in front of the mosque several blocks away.
Mohammed Abu Yusuf, 67, a travel consultant and a longtime resident, said he came out because the shooting had angered him. “Here, it is surprising,” he said.
Many people said that the nature of the shooting, in the middle of the day with no obvious motive, led them to conclude that the men were targeted because of their race or religion. “It could have been me over here,” said Kobir Chowdhury, 40, the president of Masjid Al-Aman, a nearby mosque in Brooklyn.
Zead Ramadan, the board president of the Council on American-Islamic Relations in New York, connected it to the current political discourse, where anti-Muslim rhetoric and a rise in Islamophobia have left many feeling strained. “This is a crime against humanity,” he said.
In the United States, there has been an average of 12.6 suspected anti-Muslim hate crimes a month in recent years, according to an analysis of F.B.I. statistics, but that number appeared to spike late last year.
“Of course we’re afraid,” said Jamil Kahn, 38, who has attended Mr. Akonjee’s mosque and who works in the neighborhood.
Those who knew and worshiped with Mr. Akonjee described him as a quiet and pious man. “He doesn’t talk, unless he acts,” Mr. Abdin said. “He just comes to the mosque and comes home.”
Out of many imams, Mr. Chowdhury said, “he was a imam who you would want to hear his sermon.”