Abstract Algeria is the largest country in Africa and contains a rich and understudied faunal biodiversity. Two species of hedgehogs occur in the country: the North African hedgehog Atelerix algirus and the desert hedgehog Paraechinus aethiopicus . We investigated the genetic and phenotypic variation of the two species in Algeria using mitochondrial DNA and external morphological characters. The mitochondrial phylogenetic analysis identified two major clades corresponding to the two species, whereas no phylogenetic structure was observed within either species. However, analysis of the morphological data indicated the presence of two morphotypes within A. algirus . The more common and widespread morphotype agrees well with the standard description of A. algirus , while the other recognized morphotype was found almost exclusively in the Mediterranean coastal belt and is distinguishable by a combination of morphological characters. A most remarkable finding was the detection of A. algirus individuals, with taxonomic identity confirmed by both molecular and morphological data, at extralimital localities in oases deep in the Sahara. Two of these records in central Algeria extend the distribution of the species approximately 500 Km to the south. Further sampling in the Saharan oases is needed to map more precisely the new geographic distribution of A. algirus in Algeria.