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Ichnotropis is a genus of medium-sized lacertids endemic to sub-Saharan Africa, characterised by rough head shields. The genus currently comprises six nominal species distributed across much of southern, central, and eastern Africa. Some species are apparently active at only certain times of the year, resulting in limited specimen collections and severely hampering research. This scarcity of material has historically made comprehensive systematic reviews of the genus difficult and has led to the description of numerous regional morphological variants as distinct species or subspecies. Material collected in recent years has enabled us to provide a new phylogenetic hypothesis of Ichnotropis using two mitochondrial genes (16S and ND4) and two nuclear genes (c-mos and RAG-1). Our phylogenetic dataset includes 56 individuals representing five of the six currently recognised species (excluding I. chapini). Additionally, the broad geographical sampling of the widespread I. capensis group has allowed us to explore the taxonomic status of several species and subspecies within the group. As a result, we demonstrate the monophyly of Ichnotropis in relation to other African lacertids and present the most comprehensive phylogeny of the genus to date. We also provide the first phylogenetic placements for I. tanganicana and I. grandiceps, which allows us to validate their taxonomic statuses. Furthermore, we recovered a new cryptic species closely related to I. grandiceps, and identified several well-supported clades within the I. capensis group, all corroborated by multi-locus species delimitation analyses. One of these clades is described herein as a new species, while the remaining taxa of interest are discussed and highlighted for future investigation. Based on our findings, we recommend the following taxonomic revisions: Ichnotropis longipes and I. macrolepidota should remain synonyms of I. capensis; I. bivittata pallida and I. capensis nigrescens are treated as a junior synonyms of I. bivittata; and I. overlaeti is considered a junior synonym of I. tanganicana. Although we could not determine the phylogenetic placement of I. chapini due to the lack of genetic material, its head morphology and scalation support its reassignment to the I. bivittata group. Thus, it is retained as a valid species pending the availability of new material for further taxonomic actions. In conclusion, this study resolves several long-standing taxonomic issues within one of Africa’s most understudied lacertid genera and lays a solid foundation for future research on the genus Ichnotropis.