The ship caught fire while docked at the Tenth Avenue Marine Terminal around 2:30 p.m. and was extinguished about 40 minutes later, authorities said.
The fire sparked below deck in a chemical storage area and is believed to have been caused by an electrical problem.
No injuries were reported. About 30 crew members evacuated the ship.
A hazmat team made sure there were no chemical spills in the bay.
“There were no materials that had to be discharged into the bay. That’s really important because any time you have water going into the bay you have to monitor it for environmental effects. In this case, they were able to extinguish it using CO2 gas which is harmless once it dissipates,” said Tanya Castaneda with the Port of San Diego.
The Dorado Discovery is a 321-foot Scottish-flagged minerals research vessel that arrived in San Diego last week to do exploration off the coast of Mexico.