The only species of the genus Triops in Australia, T. australiensis, is found to reproduce by gonochorism. Morphological and reproductive data and molecular analyses of fragments of mitochondrial genes 12S rRNA (12S) and cytochrome oxidase I (COI) indicate that a Triops population from the middle Paroo in north-western New South Wales is composed of two different entities, Triops cf. australiensis lineage A, and T. cf. australiensis lineage B. Gonad histology in individuals with ovisacs of lineage A revealed no evidence of testicular tissue; however, large testicular lobes were found in individuals with ovisacs of lineage B, indicating that they were anatomically hermaphrodites. This is the first record of Australian hermaphroditic Triops. For each lineage, a single haplotype of each gene was obtained. Molecular genetic distance and phylogenetic analyses confirmed the closer relationship and monophyly of the two lineages with T. australiensis (GenBank) when compared with Triops species from other continents. COI haplotypes of lineage A and lineage B differed by 7.7% from each other and differed by 10.2% and 9.6% from a published T. australiensis sequence, respectively. The 12S haplotypes of lineage A and lineage B differed by 3.3% from each other and differed by 2% and 2.5% from a published T. australiensis sequence, respectively. Our results suggest that the two co-occurring Triops lineages probably represent two species that are distinct from T. australiensis.