Australian salt lakes contain a diverse range of endemic invertebrates. The brine shrimp Parartemia is among the most speciose and salt-tolerant of these invertebrates. The morphotaxonomy of Parartemia is well established but there has only been limited molecular assessment of the phylogenetic relationships and boundaries of the morphospecies. We used multiple genetic markers (nuclear 28S and mitochondrial 16S and COI) and tree-building methods (Bayesian inference and maximum likelihood) to investigate the phylogeny of Parartemia. We also used species delimitation methods to test the validity of morphological species designations. The data set included all but 2 of the 18 described Parartemia morphospecies, collected from a total of 93 sites from across southern Australia plus some sequences from GenBank. The results identified large amounts of molecular divergence (e.g. COI P-values of up to 25.23%), some groups of closely related species (which also usually shared some morphological similarities) and some distinctive species, although the relationships among divergent lineages were generally not well resolved. The most conservative set of results from the species delimitation analyses suggests that the morphotaxonomy is largely accurate, although many morphospecies comprised divergent genetic lineages separated by COI P-values of up to 17.02%. Two putative new morphospecies, three cryptic species and one synonymy were identified. Our findings improve the knowledge of Parartemia taxonomy and will facilitate the development of future studies and conservation of this taxon.