The Chrysochloridae (golden moles) is a family of highly threatened fossorial small mammals endemic to sub-Saharan Africa. Research concerning these enigmatic animals has been limited, and there is a general dearth of biological information for most species. Clarifying the taxonomy of this afrotherian family is needed to inform conservation prioritization. Amblysomus hottentotus (Least Concern, IUCN 2016) is one of only two geographically widespread chrysochlorids, and one of five golden mole species endemic to the Greater Maputaland-Pondoland-Albany (GMPA) region of vertebrate endemism. We collected samples from 50 sites across the distribution range of Amblysomus, with emphasis on A. hottentotus, to test for cryptic diversity and to better understand diversification within the genus. Phylogeographic analyses using mitochondrial DNA and nuclear intron data revealed that A. hottentotus comprises several distinct lineages, or evolutionarily significant units (ESUs), some with restricted geographic ranges and thus worthy of conservation attention. Molecular dating suggests early-Pliocene divergence of the major lineages, with later radiations during the late-Pliocene to early-Pleistocene. Amblysomus hottentotus appears to represent a species complex, highlighting the need for a taxonomic revision of the genus. In a pilot study using ddRAD-Seq, we demonstrate the utility of this reduced-representation genome sequencing method for assessing phylogeographic structure in Amblysomus. The distinctiveness of some A. hottentotus lineages is confirmed, but there is also evidence of some incomplete lineage sorting or ongoing gene flow between two of the newly discovered ESUs. Finer-scale analyses are required to elucidate speciation and population genetic structure in this potentially speciose genus.