Branchinella longirostris is a fairy shrimp endemic to ephemeral pools on granite outcrops in southwestern Australia. The patchy nature of its habitat is thought to result in a high degree of subdivision among populations, potentially promoting speciation. We combined traditional taxonomy with a molecular phylogeny of cytochrome c oxidase I (COI) to test whether B. longirostris could be a species complex and whether the frontal appendage on the second antennae of males is a suitable character to differentiate new species. We also used nested clade analysis to assess the population structure and demographic factors explaining the geographical distributions of the mt DNA haplotypes. The results show that shapes of frontal appendages are not congruent with the mitochondrial genetic structure; however, they are positively correlated with geography. We conclude that the frontal appendage in B. longirostris is either subject to selection or a result of morphological plasticity; thus, its use in taxonomy remains uncertain. The intraspecific divergence in B. longirostris (≤7.7%) was approximately one third as large as the divergence from the outgroup (17.8–20.8%) and well within the ranges of divergence found in other crustaceans with fragmented population structure. There is some association between genetic structure and geography, resulting in the inference of restricted gene flow with isolation by distance and allopatric fragmentation as the most suitable models of the historical population processes. It is likely that the current distribution of haplotypes resulted from the dispersal of resting eggs by stochastic events (wind, birds) rather than from a fragmentation of previously continuous habitat as the estimated evolutionary age of the species (≤6.1 my) is much younger than its habitat (50–100 my). We found some evidence on the genetic level to support the hypothesis that B. longirostris could be a complex of species; however, the lack of correlation between the genetic pattern and the reproductively important frontal appendage lends a support to a view that B. longirostris is a single species with an exceptionally high intraspecific diversity.