The single-engine, fixed wing aircraft was found in the water four miles north of Mattituck around 10 a.m., according to the Federal Aviation Administration. The plane was homemade, complete with what appeared to be a parachute, and built from a kit sold by a company called Raven Aircraft.
The Coast Guard began searching the area after receiving a call shortly before 9 a.m. from another aircraft that reported seeing what appeared to be a small plane go into the water about eight miles off shore.
The agency said a short time later that a man's body had been recovered from the water. Southold police identified the pilot as 41-year-old Zubair Khan of New York City.
Rescue crews from the Coast Guard's New Haven station responded, as did Southold EMTs, the Suffolk County police marine unit and representatives from the FAA and National Transportation Safety Board.