Three new monorchiid trematodes are reported from fishes of the families Nemipteridae and Pomacanthidae; two species are described from the southern Great Barrier Reef and the third from off Moorea, French Polynesia. Allobacciger polynesiensis sp. nov. is described from Centropyge flavissima (Cuvier), Allobacciger brevicirrus sp. nov. from Scolopsis bilineata (Bloch) and Scolopsis margaritifera (Cuvier), and Allobacciger annulatus sp. nov. from Centropyge tibicen (Cuvier), Centropyge vroliki (Bleeker) and Centropyge bicolor (Bloch). The three species most closely resemble the type-species, Allobacciger macrorchis Hafeezullah & Siddiqi, 1970, as well as Allobacciger centropygis Machida & Uchida, 2001, differing primarily in the morphology of the terminal genitalia and excretory vesicle. With the introduction of these new species, the most recent generic concept does not accurately reflect all species in the genus, and we provide a revised generic diagnosis to accommodate the new taxa. Complete ITS2 rDNA, partial 28S rDNA, partial 18S rDNA and partial cox1 mtDNA sequence data were generated for the three new species; all markers distinguish the three species reported here unambiguously. Phylogenetic analyses of the new sequence data show that the three new species of Allobacciger Hafeezullah & Siddiqi, 1970 form a well-supported clade.