The medically important scorpion genus Hottentotta Birula, 1908 has long been a taxonomical challenge. This species-rich scorpion genus contains three lineages spread over most of Africa and part of Asia. The Maghrebian Hottentotta was historically recognised as a single species, H. franzwerneri (Birula, 1914), divided in two subspecies with disjunct distributions. A recent morphological study raised both Maghreb subspecies to species level, H. franzwerneri and H. gentili (Pallary, 1924). In this study we assess the phylogenetic relationships between specimens of the genus Hottentotta from Morocco using cytochrome oxidase 1 (CO1) mitochondrial DNA sequences. Our finding of H. gentili in the eastern portion of Morocco increases the known range of this taxon and significantly reduces the geographic distance that separates it from H. franzwerneri. Furthermore, we found four well supported clades in the Maghrebian Hottentotta. All H. franzwerneri specimens group in the franzwerneri clade, but H. gentili specimens group in three different clades. The Ziz valley clade form a sister group to the franzwerneri clade, specimens from the core range of H. gentili group in the central clade, while specimens from the southern distribution of the species group in the Low Draa valley clade, basal in our tree. These findings challenge current Hottentotta taxonomy because they imply paraphyly of H. gentili, although mitochondrial introgression cannot be excluded. Further studies are needed to fully comprehend the taxonomy of Hottentotta from this region and the role that colour characters play in scorpion species diagnoses.