Patterns of biodiversity and evolutionary processes controlling them are still poorly studied in desert biomes. Fine-scale markers could help answer some of the pressing research questions for desert biomes and Sahara in particular. Such markers are available for some large mammals and crocodiles, but not for small vertebrates. Here we present a battery of microsatellite loci developed for Agama boulengeri, a promising model to study evolutionary and demographic processes in the Sahara-Sahel. Loci were selected by sequencing enriched DNA libraries with 454 pyrosequencing. A total of 23 polymorphic loci were successfully amplified in four multiplex reactions. Cross-amplification of the microsatellite loci in A. agama and A. boueti was partially successful. These markers are a promising tool for assessing genetic diversity, gene-flow dynamics and demographic patterns in this group. Given the genus Agama is distributed throughout Africa, results presented here might also facilitate studies in other regions.