A 2007 study of Suminoe (Crassostrea ariakensis) and eastern (Crassostrea virginica) oysters exposed to Indian River Lagoon (IRL), Florida waters revealed the presence of Bonamia spp. in exposed oysters. In 2010, a survey of oysters and other bivalves (n = 721, 18 species) was conducted in the southern IRL (10 sites) and in the more southerly Lake Worth Lagoon (LWL, 3 sites). Polymerase chain reaction (PCR) was used to assess the prevalence of three oyster parasites, Bonamia spp., Perkinsus marinus, and Haplosporidium nelsoni, in collected samples. Histology, fluorescent in situ hybridization (FISH) and standard H&E staining, was used to confirm PCR-positive Bonamia results. Bonamia spp. was detected in eight species (Brachidontes exustus, Crassostrea virginica, Geukensia demissa, Ischadium recurvum, Isognomon alatus, Isognomon bicolor, Mercenaria campechiensis, and Ostrea stentina). The prevalence was 17.3% in the IRL and 9.9% in LWL with 66% of PCR-positive samples subsequently identified as either Bonamia exitiosa or Bonamia perspora. The presence of Bonamia spp. was confirmed by FISH in C. virginica, O. stentina, I. alatus, I. bicolor, and G. demissa, although only C. virginica and O. stentina showed evidence of infection. The presence of P. marinus was detected in eight species (Atrina rigida, B. exustus, C. virginica, G. demissa, I. recurvum, I. alatus, I. bicolor, and O. stentina). The prevalence was 12.4% in the IRL and 7.7% in LWL. The presence of MSX was not detected in any of the collected bivalves. This study confirms the presence of Bonamia spp. and P. marinus in Florida east coast waters and widens the described geographic range for Bonamia spp., and provides further evidence that MSX is unlikely to be found in Florida waters