Coral bleaching involves the loss of symbiotic algae (zooxanthellae) from reef corals and other cnidarians during periods of environmental stress, particularly elevated temperature. In this study we compared the thermal bleaching responses of the zoanthid Palythoa caribaeorum from three populations along the southeast coast of Florida. Winter (2002-2003) and summer (2003) samples from three geographically separate sites were experimentally exposed to increased temperatures and the loss of zooxanthellae was measured. Population densities of zooxanthellae were analyzed and their genetic identity determined using PCR-DGGE analysis of the internal transcribed spacer region 2. The results showed that samples of P. caribaeorum from reefs that experienced the smallest range in annual seawater temperature released the most zooxanthellae. Seasonal comparisons revealed that winter samples lost more zooxanthellae than summer samples. P. caribaeorum harbored two genetic types of zooxanthellae, C1 and D1a. Individual colonies contained populations of only C1 or D1a, or combinations of C1 and D1a. However, these genotypic patterns did not relate latitudinal distribution nor to differences in experimental thermal tolerance. © 2006 Elsevier B.V. All rights reserved.