The pouched mouse, Saccostomus campestris Peters, 1846 from southern Africa shows a high degree of karyotypic variation where up to 16 variants (2n = 30–50) have been reported. This has led to a systematic uncertainty that the present study attempts to assess using: 1) cytochrome b (cyt b; 1077 bp) and 16S rRNA (528 bp) partial sequences; 2) G-banding cytogenetic data; and 3)geometric morphometric data of various views of the cranium and mandible. The results from these multidisciplinary analyses are broadly similar with phylogenetic analyses of the molecular data revealing the presence of two major lineages. The first lineage comprises the high diploid numbered 2n = 46 cytotype from KwaZulu-Natal Province, South Africa that is considered to be ancestral. The second lineage consists of multiple inland populations that are subdivided into: 1) a sub-lineage comprising samples from a large semi-arid area in the west; and b) a sub-lineage of small distinct populations of low migrations from the east. The cytogenetic data suggest that karyotypic variation within S. campestris from southern Africa is due to autosomal Robertsonian fusions, with evidence of geographic structuring where cytotypes with high diploid numbers originate from the mesic east, while those with low diploid numbers originate from the arid west. The reduction in chromosome number appears to be due to adaptation to cold and dry conditions in the arid west. The X-chromosome revealed three variants that arose from a single pericentric inversion followed by the addition of genetic material, possibly heterochromatin. Variant 1 is only present in the ancestral cytotype and is found in all cytotypes throughout southern Africa, variant 2 is found in cytotypes from areas with < 600 mm of annual rainfall, while variant 3, although only found in females, is sympatric with variant 2. Geometric morphometric analysis of karyotyped specimens showed no discernible patterns of variation among karyotypic variants except for some subtle but equivocal indication of the morphological distinctiveness of the 2n = 46 cytotype from KwaZulu-Natal. Collation of the molecular, cytogenetic, and geometric morphometric data in the present study suggest that S. campestris from southern Africa is monotypic.