Emil Benjamin, 39, was arrested on charges of hate crime and burglary, police announced Thursday.
Benjamin is suspected vandalizing four different synagogues located at 1694 Ocean Avenue, 2822 Avenue J, 2201 Avenue L and 1720 Avenue J.
Police say the graffiti included derogatory phrases.
At the synagogue on 1720 Avenue J, Benjamin is accused of illegally entering the synagogue and making graffiti inside before damaging two cabinets and stealing $20.
New York Governor Andrew Cuomo had directed the state police Hate Crimes Task Force to assist the NYPD in the investigation.
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