Primers to amplify partially the mitochondrial genes coding for cytochrome b, 12S-rRNA and the D-loop were screened in twelve small mammal species from southern Africa. We also tested the possibilities of molecular sex identification using primers of the SRY. The study includes five species of murids of the genera Aethomys, Thallomys, Rhabdomys and Saccostomus, four gerbils of the genera Desmodillus, Tatera, Gerbillurus, one dormouse (Graphiurus) and two macroscelids (Macroscelides and Elephantulus). We provide information on the primers with modifications, lab protocols and we give an overview of the obtained sequences: four cytochrome b sequences and five 12S-rDNA sequences of three species and 23 D-loop sequences of five species. Sex specific fragments of SRY could be amplified in three species of Murinae and the dormouse.