Coral reefs are some of the most diverse ecosystems in the world and provide economic value as well as biodiversity stability. Yet, these ecosystems are threatened from human degradation and climate change. Phylogenetic reconstructions can help identify which species have a potential to undergo greater amounts of change in the near future and also aids in determining evolutionary distinctiveness, which are critical components of conservation management. However, traditional Scleractinia morphological characters have been shown to have limited taxonomic use. Therefore, this study attempts to discover soft tissue characters to produce more robust phylogenies. Eight coral species from the Indo-Pacific families Merulinidae and Lobophylliidae were mail ordered and prepared for histological analysis under light microscopy. A character matrix was analyzed and the results were compared to phylogenies based on skeletal and molecular data. A total of seven MPTs of length 35, C.I. 0.60 and R.I. 0.58 were found. In addition, a detailed description of the histology is included. The topology of MPTs was inconsistent, but several were broadly similar to previous phylogenies based on molecular and skeletal data. Still, using only a small number of characters, the results do promise that histological characters in conjunction with skeletal characters could better delineate species and their evolutionary history. Future results could aid in making conservation decisions based on improved phylogenies.