The distribution of the scorpion genus Buthus Leach, 1815 includes southwestern Europe, North and Central Africa and extends east towards the Arabian Peninsula. Phylogenetic relationships within the genus are complex and remain partially unresolved despite several previous assessments. A set of three mitochondrial markers, 12s, 16s and CO1, revealed the presence of five well-supported clades: three clades endemic to Morocco, one clade distributed across the Maghreb region and southwestern Europe and one endemic to Tunisia and Algeria. Morocco presents high levels of endemism and appears to be the centre of diversity for the genus. Further differentiation was found within the clade distributed in Tunisia and Algeria, with the discovery of new phylogenetic patterns. In addition, a phylogeny combining all published CO1 data for the genus emphasized the ongoing complex situation regarding the genus' taxonomy. Highly similar sequences were attributed to different species by different authors throughout the tree, and no differentiated monophyletic species could be resolved. This lack of congruence between morphologically defined species and genetic lineages is a major hindrance in the study of the highly complex genus Buthus.