Maximum growth rate and toxin content were significantly different among five strains of Karenia brevis isolated from Texas and Florida when grown under identical culture conditions. Sequence analysis of the 18S rRNA gene and internal transcribed spacer (ITS) regions revealed, however, that all five strains were identical. Consequently, a clear genetic basis for physiological variability among various geographical isolates of K. brevis from the Gulf of Mexico could not be assessed using these genetic markers. Both the ITS and 18S rRNA regions may be useful in species-specific probe selection. At the intra-specific level, however, an alternative marker will be needed to assess the diversity among K. brevis populations in the Gulf of Mexico.