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).