Golden moles (family Chrysochloridae) belong to Afrotheria, an ancient clade of placental mammals that ranks among Africa’s most enigmatic and endangered, but poorly studied endemic mammals. Two subfamilies, 10 genera and 21 species are recognized, of which 10 species are threatened (IUCN 2016). Nonetheless, unclear taxon delineations based on morphology, cytogenetics and limited molecular data have hitherto impeded conservation efforts. Within this context, we present a fully-resolved chrysochlorid phylogeny based on a concatenation of molecular (five genes) and multistate morphological and cytogenetic characters (32) using model-based Bayesian and maximum likelihood inference.These analyses uncovered genetically distinct lineages within two genera and cryptic lineages within three species, which form the basis of a revised Chrysochloridae classification presented here. As the phylogeny offers unique insights into the diversification of an old but range-restricted clade across the African continent, we used molecular dating to place the evolutionary radiation of chrysochlorids in the context of Africa’s palaeoclimatic and geological history. We also present a novel molecular phylogenetic framework based on mitochondrial and nuclear genes for one of Africa’s most threatened small mammals, Neamblysomus julianae, that is known from only three range-restricted and geographically isolated populations revealed three genetically unique lineages, one of which is highly divergent, which informed conservation planning for the species that should be aimed at conserving the integrity of each genetically unique population. Rigorous geographic sampling chrysochlorids, and species in general.