[Truncated abstract] I have evaluated the effects of different types of ephemeral pools on the evolutionary dynamics of two large branchiopods in Australia, the clam shrimp Lynceus and the fairy shrimp Branchinella longirostris. Both shrimps are passive dispersers, relying on their sexually produced resting eggs for continuity of populations in time and space, although their actual dispersal ability remains speculative. The two currently recognised species of the genus Lynceus (L. tatei and L. macleyanus) are widespread across Australia, and they occupy a wide range of ephemeral fresh water habitats, while the fairy shrimp Branchinella longirostris is endemic to rock pools on granite outcrops in south-western Australia. Samples of populations were collected from a total of 96 ephemeral pools at 80 locations in New South Wales, Northern Territory, Queensland, South Australia and Western Australia . . . This highlighted the contrast between the two species and their microhabitats, and implied that these microhabitats offered different opportunities for dispersal. These were identified as frequent disturbances of the clam shrimp’s egg-banks due to ‘wash-out’ effects during heavy rains and animal and human vectors attracted by the water stored in the deep pools. My comparative study shows that the difference in evolutionary dynamics observed between the two species was a consequence of their environmental interactions rather than of the microhabitats themselves. Similar to patterns detected in other passive dispersers with disjunct population distribution, evolutionary dynamics in Lynceus and B. longirostris seem to be a result of complex interactions among gene flow, population histories and ecology of their habitat. The results contribute to the emerging evidence that branchiopod crustaceans are poor dispersers and highlight the importance of local context in determining evolutionary processes within species.