Clinostomum Leidy, 1856 (Trematoda: Clinostomidae) is a cosmopolitan, zoonotic genus of fluke that has been poorly studied in an Australian setting. Following previous reports of reservoir fish in Australian fish ponds being heavily infected with Clinostomum metacercaria, the current study was conducted to determine the specific identity of Clinostomum sp. in inland Australia, by examining and characterizing parasites collected from a potential definitive host, cormorants. A total of 33 parasite specimens belonging to the genus Clinostomum were collected from two cormorants (little black cormorants, Phalacrocorax sulcirostris) that were collected from the Narrandera Fisheries Research Centre, New South Wales, at the same locality where metacercaria of Clinostomum sp. have been reported in fish. All specimens in our study were immature adults. Clinostomum specimens with similar morphology have been identified as C. complanatum in the past, based on their morphological characteristics. However, phylogenetic analyses based on the ITS sequence data in the present study suggest they are the same as the Clinostomum sp. previously reported from carp gudgeons (Hypseleotris spp.) from the same farm, and distinct from C. complanatum. The ITS sequences obtained from the specimens in the present study were most similar to those belonging to C. phalacrocoracis (never reported in Australia). Our specimens formed a distinct clade on the phylogenetic tree and their specific identity awaits until fully mature specimens are described in future studies.