The Fresno County Sheriff's Office has identified the man as 53-year-old Steven Wilson of Shafter, California.
Deputies received a report of the missing aircraft around 11 pm on Tuesday after a crop-dusting company said it lost contact with a pilot. They had been searching for the crop-dusting helicopter and its pilot all night.
At around 3 am Wednesday, a fixed-wing plane involved in the search spotted the helicopter in an orchard near Sonoma and Chandler, northeast of Coalinga near Harris Ranch.
Wilson was the only person onboard the aircraft
Investigators with the FAA and the National Transportation Safety Board (NTSB) are traveling from Arizona.
The NTSB will be in charge of the investigation.