Zooxanthellate soft corals are among the most ecologically important and dominant benthic organisms on tropical reefs of the Indo-Pacific. Previous taxonomic studies have described around 600 taxa of these sessile, photosymbiotic macro-organisms. However, identification of species based on morphology can often be unreliable and complicated by the group’s phenotypic plasticity; this difficulty inhibits our understanding of the reef’s ecology. Xeniidae and the Alcyoniidae are the two most diverse families of zooxanthellate soft corals. We used the molecular barcode mtMutS, a mitochondrial gene, to assign xeniids and alcyoniids to molecular operational taxonomic units (MOTUs) as proxies of species. With these assignments we surveyed the distribution of the two families throughout the Indo-Pacific. Cluster analysis suggested that there is little overlap in MOTU composition between the Indian Ocean and Pacific Ocean. Mantel regressions indicate a highly significant relationship between MOTU composition and the geographic distance between two collection sites, with closer sites sharing more species than distant sites. The strength of that relationship differed between the families, possibly due to their different reproductive strategies. Xeniids brood their larvae, leading to lower dispersal and more endemic species. Alcyoniids are broadcast spawners, which leads to higher dispersal and fewer endemic species. Regardless of reproductive strategy, the data suggest that the geographic ranges of species in both families are smaller than those commonly suggested by most taxonomic literature.