The Enenteridae Yamaguti, 1958 and Gyliauchenidae Fukui, 1929 exhibit an interesting pattern of host partitioning in herbivorous fishes of the Indo-West Pacific. Enenterids are known almost exclusively from fishes of the family Kyphosidae, a group of herbivorous marine fishes common on tropical and temperate reefs. In contrast, gyliauchenids are found in most of the remaining lineages of marine herbivorous fishes, but until the present study, had never been known from kyphosids. Here we report on the first species of gyliauchenid known from a kyphosid. Endochortophagus protoporus gen. nov., sp. nov. was recovered from the Western buffalo bream, Kyphosus cornelii (Whitley, 1944), collected off Western Australia. Kyphosus cornelii also hosts an enenterid, Koseiria allanwilliamsi Bray & Cribb, 2002, and is thus the first fish known in which enenterids and gyliauchenids co-occur. Molecular phylogenetic analyses place the new species close to those of Affecauda Hall & Chambers, 1999 and Flagellotrema Ozaki, 1936, but there is sufficient morphological evidence, combined with the unusual host, to consider it distinct from these genera. We discuss factors which may have contributed to the host partitioning pattern observed between enenterids and gyliauchenids.