Gymnocins are a series of cytotoxic polyether compounds isolated from the notorious red tide dinoflagellate Karenia (formerly Gymnodinium) mikimotoi. Among them, the structures of gymnocin-A and gymnocin-B have already been elucidated. Gymnocin-A carboxylic acid and a new analog of gymnocin-A, gymnocin-A2, were isolated from K. mikimotoi cells, and their structures were determined by detailed analysis of 2D-NMR spectra. The structural changes of gymnocin-A carboxylic acid and gymnocin-A2 occurred on the terminal side chain and ring A in gymnocin-A. Gymnocin-A carboxylic acid and gymnocin-A2 showed moderate cytotoxicity against P388 cells.