Freshwater species are expected to show higher levels of genetic structuring than those inhabiting estuarine or marine environments because it is difficult for freshwater species to move between river systems. Previous genetic studies of freshwater species from coastal streams in south-east Queensland had proposed that several of these streams had a common confluence relatively recently, when sea levels were lower ~10 000 years bp. The present study was undertaken to test this idea using two freshwater shrimp species, Macrobrachium australiense and Macrobrachium tolmerum. In M. australiense, there was a major phylogeographical break in the middle of the Sunshine Coast region that was expected to be homogeneous because these creeks may have had a shared confluence before entering the sea, possibly because of extremely limited dispersal abilities compounded over many generations. In M. tolmerum, there was evidence of a recent population expansion and also some evidence of limited gene flow between sites. This is explained by recent colonisation of the area and limited gene flow between river systems, despite the ability of this species to survive in brackish water conditions. The present study shows that even species that are taxonomically very close and that co-occur in the same habitats can have vastly different population structures.