Using range-wide sampling and 1,143 bp of mtDNA (cytochrome b gene) and 14 microsatellite loci, we examined genetic differentiation in the widely distributed Southern African angulate tortoise (Chersina angulata). We found evidence for two genealogical lineages that differ in both genetic marker systems and their preferred habitat conditions. According to a fossil-calibrated molecular clock for all African tortoise lineages using 1,870 bp mitochondrial and 1,416 bp nuclear DNA, the two lineages of C. angulata diverged in the Pliocene (approx. 3.8 million years ago). Species distribution models reveal that the ranges of the two lineages shifted little since the Last Glacial Maximum, which is in agreement with the demographic population descriptors suggestive of stationary populations that did not experience expansion. One lineage occurs in the west, and the other in the south of the extant distribution range. In the geographic contact zone, the two lineages hybridize extensively, providing evidence for their conspecificity under the biological species concept. Each lineage could be recognized as a distinct subspecies, but the ill-defined geographic origins of the type material of the available names prevent their identification with any taxon. With respect to the nuclear genomic markers, the western lineage shows further north-south substructuring. A few genetically mismatched tortoises are interpreted as human translocations. Our study underlines that confiscated or captive angulate tortoises of unknown geographic provenance should not be released without prior genetic screening to avoid genetic pollution of wild populations.