We examined range-wide mitochondrial phylogeographical structure in the riverine freshwater turtle Chelodina expansa to determine whether this species exhibits deep genetic divergence between coastal and inland hydrological provinces, as seen in co-distributed freshwater taxa. We sequenced two mitochondrial loci, genealogical relationships were assessed using a network approach, and relationships among biogeographical regions were tested using analyses of molecular variance. Population history was evaluated using neutrality tests, indices of demographic expansion, and mismatch analyses. Twenty-one haplotypes were recovered across two mitochondrial haplogroups separated by approximately 4% nucleotide divergence. The haplogroups have discrete geographical boundaries but only partially support a hypothesis of deep divergence between coastal and inland bioregions. The first haplogroup comprises populations from the inland Murray-Darling Basin and from coastal catchments south of the Mary River in south-east Queensland. The second haplogroup comprises populations from coastal catchments north of the Mary River. Cryptic phylogeographical barriers separating adjacent coastal populations are congruent with those demonstrated for other freshwater taxa and may result from the combined influences of the Conondale Range and alluvial deposits at the mouth of the Mary River. The findings of the present study demonstrate that freshwater taxa commonly display genetic differentiation within a biogeographical region where no boundaries have been recognized, highlighting the need to uncover cryptic microbiogeographical regions to aid conservation of freshwater biota.