Due to morphological comparisons the Tunisian desert ant species Cataglyphis bicolor has been divided into three parapatric species: C. bicolor, C. viatica, and C. savignyi. The species status of the latter is supported by sequence analyses of the mitochondrial CO1 and CO2 region, while analyses of the same mitochondrial region lacked resolution for the separation of C. bicolor and C. viatica. However, the geographic distribution of mtDNA haplotypes points to different population viscosities with C. bicolor queens having longer migration distances than queens of C. viatica. Furthermore, by the use of microsatellites we excluded ongoing gene flow between geographically overlapping populations of C. bicolor and C. viatica, and hence support the morphology-based three-species hypothesis. Concerning the ongoing discussion on the future roles of morphology and molecular biology in systematics we call for a combination of both whenever possible.