Contributing to the knowledge of digenetic trematodes in northern Australia, this study uses both morphological and molecular analysis to augment the taxonomic descriptions of existing digenean trematodes from the black-spotted croaker, Protonibea diacanthus (Lacepède, 1802) (Teleostei: Sciaenidae) from waters off northern Australia. Using a combination of morphological and molecular techniques, Orientodiploproctodaeum diacanthi Bhutta and Khan, 1970 (Digenea: Cryptogonimidae) and Pleorchis sciaenae Yamaguti, 1938 (Digenea: Acanthocolpidae) are compared with closely related specimens representing new geographical records of these species, and contributing the first phylogenetic analysis of both digenean species. Both O. diacanthi and P. sciaenae were genetically distinct from other reported specimens of the respective families Cryptogonimidae and Acanthocolpidae, based on phylogenetic results and the supporting morphological descriptions from past publications. Despite the conclusive findings in this study, the species presented in the phylogenetic analyses lack sequences across a range of genes, leading to difficulties in deciphering the phylogenetic and evolutionary relationships of many species and highlighting the need for future research to improve species-level identification of parasites in Australian waters.