Marine shellfish exposed to the microalgae Karenia selliformis can accumulate gymnodimines (GYM). Shellfish samples collected from Beihai City in Guangxi Autonomous Region, and Ningde City in Fujian Province, in the South China Sea, as well as mussels Mytilus galloprovincialis fed on K. selliformis under laboratory conditions were analyzed. Gymnodimines and various fatty acid ester metabolites were detected in the clam Antigona lamellaris and pen shell Atrina pectinata, while no esters were found in the oyster Crassostrea sp. and the gastropod Batillaria zonalis despite positive detection of free GYM in both species. When present, the predominant acyl esters observed were 18:0-GYM-A and 20:1-GYM-A. Under laboratory conditions GYM-A was accumulated and metabolized to fatty acid esters in mussels exposed to K. selliformis, with 16:0-GYM-A and 20:1-GYM-A as the major variants. A novel compound with the same accurate mass as GYM-A and its 16:0 fatty acid ester were observed in the experimental mussels but was not present in the microalgal strain to which mussels were exposed. No significant differences of reactive oxygen species (ROS) levels and antioxidant enzymes were found between mussels fed on K. selliformis or GYM-free microalgae Isochrysis galbana. This suggests the accumulation of GYM and its metabolites does not significantly impact the physiological status of mussels. While it is currently not proven that GYM affects human health, risk assessments should consider the presence of GYM esters in naturally contaminated shellfish as part of exposure analysis.