Eight boats and a helicopter are covering an area of about 60 sq miles (155 sq km) off Anglesey.
A call was made at 02:29 GMT after reports of a man going overboard a fishing vessel. He was last seen at 00:45 GMT.
Porthdinllaen and Trearddur Bay lifeboats, along with the inshore lifeboat, have also joined the search.
Ray Carson, rescue co-ordination manager for Holyhead coastguard, said: "The vessel left Holyhead at 23:25 GMT to go around into Caernarfon Bay.
"The missing person was last seen in the galley at 00:45. The vessel was 1.2 miles west of South Stack lighthouse, near Holyhead."
Mr Carson said it was about 15 miles off the coast when the mayday call came in.
He added a planning computer looking at winds and tidal currents was being used to work out where the missing fisherman might be.
"Initially the search was undertaken by Rescue 122 helicopter from Valley and the Holyhead RNLI all-weather lifeboat," he said.
"They both searched from the South Stack to the mayday position.
"We also brought out Porthdinllaen lifeboat, and they were joined by three other fishing vessels and the casualty vessel.
"They searched in a line working northwards up to South Stack from the mayday position."
Mr Carson told BBC Wales the helicopter had returned to RAF Valley for refuelling while the boats continued to search the area.
He said sea conditions were "favourable".