Samples from 83 populations of salt lake Ostracods belonging to the genus Mytilocypris were collected from 74 saline lakes and ponds in the semi-arid regions of Australia. These populations were examined for variation at six polymorphic enzyme loci to diagnose breeding systems and to measure population structure, to investigate relative levels of gene flow in species with differing distributions and hence different presumed dispersal capabilities. Despite the occurrence of some populations in disjunct, peripheral, and recent ephemeral habitats, all populations of each species were found to reproduce sexually. Gene flow does occur on a local basis and appears to be facilitated by occupation in the same drainage basin for some species. There was considerable gene pool fragmentation among peripheral populations of four of the five species. Only one species, M. mytiloides, was relatively homogeneous across its range. It may be that gene flow is non-existent into peripheral populations because of poor dispersal abilities, or it may not be frequent enough to overcome local selective pressures. Regardless of these possibilities, the observed gene pool fragmentation has implications for allopatric speciation.