The objective of this study is to examine the distribution patterns of apicomplexan symbionts in a diverse selection of corals from a wide depth range. We sampled corals and sequenced the plastid 16S DNA of apicomplexans found in 96 corals. The apicomplexan symbionts showed patterns of geographical, depth, and host distribution. Our results suggest that apicomplexan symbionts of corals are wide spread, horizontally transmitted, may be co-evolving with corals, and are not photosynthetic.