The document summarizes a study analyzing the morphology of zooxanthellae communities in two coral species, Montastraea cavernosa and Pseudodiploria clivosa, using FlowCAM imaging. Densities of zooxanthellae cells per square centimeter of coral tissue were measured and compared between traditional and FlowCAM methods at three sites. FlowCAM allowed for higher resolution analysis of cell volumes and chlorophyll content. Future work will involve next generation sequencing to characterize zooxanthellae clades associated with each coral species.