The aircraft was on a regular training mission Wednesday when the incident occurred about 120 miles (190 kilometers) southeast of Iwakuni, the Marine Corps said.
Joint search efforts with Japanese military ships and aircraft were carried out through the night.
The identity of the pilot has not been released.
Japan's Defense Ministry said the F/A-18 had been flying with another Marine jet.
The Corps said the aircraft was assigned to the 1st Marine Aircraft Wing in Okinawa, Japan.
It said the cause of the incident was under investigation.
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