Abstract Emprostiotrema contains just 3 species: E. fusum , E. kuntzi and E. sigani . As adults, all 3 species infect rabbitfishes (Siganidae: Siganus ). New collections from 11 species of Siganus from northern Australia, Indonesia, New Caledonia, French Polynesia, Palau and Japan enabled an exploration of species composition within this genus. Phylogenetic analyses demonstrate a deep distinction between 2 major clades; clade 1 comprises most of the sequences of specimens from Australia as well as all of those from Japan, Palau and New Caledonia and clade 2 comprises all sequences of specimens from French Polynesia, 2 sequences from Australia and the single sequence from Bali. In all analyses, both major clades have genetic structuring leading to distinct geographic lineages. Morphologically, specimens relating to clades 1 and 2 differ but overlap in body shape, oral sucker and egg size. Principle component analysis shows a general (but not complete) separation between specimens relating to the 2 clades. We interpret the 2 clades as representing 2 species: clade 1 is identified as E. fusum and is reported in this study from 10 species of siganids from Australia, Japan, Palau and New Caledonia; clade 2 is described as E. gotozakiorum n. sp., for all specimens from French Polynesia and rare specimens from Australia and Indonesia. We recognize E. sigani as a junior synonym of E. fusum . Although species of Emprostiotrema occur widely in the tropical Indo-Pacific, they have not been detected from Ningaloo Reef (Western Australia), the southern Great Barrier Reef or Moreton Bay (southern Queensland).