Coral reefs harbor the greatest biodiversity per unit area of any ecosystem on earth. While parasites constitute the majority of this biodiversity, they remain poorly studied due to the cryptic nature of many parasites and the lack of appropriate training among coral reef ecologists. Damselfishes (Pomacentridae) are among the most abundant and diverse fishes on coral reefs. In a recent study of blood parasites of Caribbean reef fishes, the first ever apicomplexan blood parasites discovered in damselfishes were reported for members of the genus Stegastes. While these blood parasites were characterized as “Haemohormidium-like”, they appear to be distinct from any other known apicomplexan. In this study, we examined host associations, geographic distributions, and provide further insights on the phylogenetic affiliation of this parasite. A combination of morphological characteristics and 18S rDNA sequences suggest that this parasite may be the same species at multiple sites and occurs from the southern to the northern extreme of the eastern Caribbean, although it appears rare in the north. At present it appears to be limited to members of the genus Stegastes and infects all life history stages. It is most common in benthophagous species that occur in high population densities and appears basal to a major monophyletic clade containing species of coccidia, distinct from the Piroplasmida, the order to which Haemohormidium spp. have been assigned. These findings suggest a possible fecal-oral mode of transmission.