We examined range-wide mitochondrial phylogeographic structure in the riverine freshwater turtle Chelodina expansa to determine if 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 biogeographic 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 ca 4% nucleotide divergence. The haplogroups have discrete geographic 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 southeast Queensland. The second haplogroup comprises populations from coastal catchments north of the Mary River. Cryptic phylogeographic 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. Our study demonstrates that freshwater taxa commonly display genetic differentiation within a biogeographic region where no boundaries have been recognised, highlighting the need to uncover cryptic microbiogeographic regions to aid conservation of freshwater biota.