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The systematics of the genus Acanthodactylus was classically based on external morphological traits, osteological characters and morphology of the hemipenes. Although the identification of species complexes is relatively easy, the distinction within some groups is difficult due to a high variability of the external morphology. Partial mitochondrial (12S and 16S rRNA) sequences (371 and 499 base pairs, respectively) were analysed from 32 specimens of the A. pardalis group from northern Africa including the described species A. busacki, A. maculatus, A. mechriguensis and A. pardalis. Several highly distinct genetic units were resolved, but with little support for relationships between them. These units did not coincide with current taxonomic units, but showed geographic structuring. Although the A. pardalis group displays significant variation, the present taxonomy of the group must be considered unsatisfactory since it is not supported by genetic evidence. For some forms, such as A. mechriguensis there is no support and it is suggested that it should be synonymized with A. maculatus. More data are clearly needed for other forms. Complex microevolutionary patterns due to the recent contraction/expansion phases of the Sahara Desert probably are related with the phylogenetic patterns observed.