The Coast Guard, New Jersey State Police and local authorities are all joining in the search.
The missing man, 45-year-old Christopher Hugg, was reported around 8 a.m. Friday.
According to the U.S. Coast Guard, Hugg reportedly contacted a relative around 8 p.m. Thursday to say his clamming boat ran aground, but he did not require assistance.
The Coast Guard said Hugg's boat was found containing fishing gear on Hither Island earlier Friday.
Rescue boats and a helicopter were deployed to search for Hugg.
However, the search was called off due to darkness Friday evening with no sign of the missing man.
Relatives say Hugg, who lives just a few miles from the search area, has been fishing in the area all his life.