The taxonomy of many Hemidactylus geckos from the Horn of Africa has recently been evaluated. However, the lack of fresh material for some species and also regions has led to the misidentification of some taxa and an underestimation of the true diversity in others. In this study we analyse new material of Hemidactylus collected from poorly known coastal areas of northern Somaliland. Our results support the existence of two yet undescribed species within the arid clade. One of the new species is small-sized and closely related to H. afarensis from the Afar Triangle in Ethiopia, and together with two other species (H. foudaii, H. sinaitus) forms the monophyletic group for which we propose here the name sinaitus species group. The other new species is medium to large-sized, known from only one locality, and belongs to the macropholis species group, where it is a sister species of H. macropholis. Both new endemic species from the northern coastal hyper-arid plains highlight the role of northern Somaliland as an important biodiversity hotspot. Furthermore, our results show pronounced genetic diversity within H. macropholis, and imply possible existence of cryptic taxa within the species. Hemidactylus arnoldi and H. tropidolepis have, for the first time, been sequenced and placed in a phylogenetic context in this study. Our results confirm that H. tropidolepis is nested within the African radiation and is most closely related to H. funaiolii. Hemidactylus arnoldi clustered within the Arabian radiation of Hemidactylus and it was recovered as a sister lineage to all other species of the radiation.