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. M. cavernosa harbored clade C zooxanthellae with larger cell volumes and more chlorophyll per cell than P. clivosa, which harbored clade B zooxanthellae. Next-generation sequencing was also proposed to further characterize the zooxanthellae communities.