Blooms of Karenia brevis, the major bloom-forming dinoflagellate in the Gulf of Mexico, are thought to originate in the eastern Gulf. Single-cell polymerase chain reaction and five microsatellites were used to obtain genotypes for >1800 cells from 38 samples collected from six bloom events. A consistent pattern of genetic divergence between blooms from Florida and Texas was not detected, which supports the hypothesis of a common origin for blooms of K. brevis in the Gulf of Mexico.