A previously unsurveyed calcrete aquifer in the Yilgarn region of Western Australia revealed an unprecedented diversity of copepods, representing 67% of that previously recorded in this whole region. Especially diverse was the genus Schizopera, with up to four morphospecies per bore and a significant size difference between them. Aims of this study were to: (1) survey the extent of this diversity using morphological and molecular tools; (2) derive a molecular phylogeny based on COI; and (3) investigate whether high diversity is a result of an explosive radiation, repeated colonisations, or both, size differentiation is a result of parallel evolution or different phylogeny, and whether Schizopera is a recent invasion in inland waters. More than 300 samples were analysed and the COI fragment successfully amplified by PCR from 43 specimens. Seven species and one subspecies are described as new, and three possible cryptic species were detected. Reconstructed phylogenies reveal that both explosive radiation and multiple colonisations are responsible for this richness, and that Schizopera is probably a recent invasion in these habitats. No evidence for parallel evolution was found, interspecific size differentiation being a result of different phylogeny. Sister species have parapatric distributions and show niche partitioning in the area of overlap.