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<p>Abstract</p> <p>Background</p> <p>The genus <it>Arachis </it>includes <it>Arachis hypogaea </it>(cultivated peanut) and wild species that are used in peanut breeding or as forage. Molecular markers have been employed in several studies of this genus, but microsatellite markers have only been used in few investigations. Microsatellites are very informative and are useful to assess genetic variability, analyze mating systems and in genetic mapping. The objectives of this study were to develop <it>A. hypogaea </it>microsatellite loci and to evaluate the transferability of these markers to other <it>Arachis </it>species.</p> <p>Results</p> <p>Thirteen loci were isolated and characterized using 16 accessions of <it>A. hypogaea</it>. The level of variation found in <it>A. hypogaea </it>using microsatellites was higher than with other markers. Cross-transferability of the markers was also high. Sequencing of the fragments amplified using the primer pair Ah11 from 17 wild <it>Arachis </it>species showed that almost all wild species had similar repeated sequence to the one observed in <it>A. hypogaea</it>. Sequence data suggested that there is no correlation between taxonomic relationship of a wild species to <it>A. hypogaea </it>and the number of repeats found in its microsatellite loci.</p> <p>Conclusion</p> <p>These results show that microsatellite primer pairs from <it>A. hypogaea </it>have multiple uses. A higher level of variation among <it>A. hypogaea </it>accessions can be detected using microsatellite markers in comparison to other markers, such as RFLP, RAPD and AFLP. The microsatellite primers of <it>A. hypogaea </it>showed a very high rate of transferability to other species of the genus. These primer pairs provide important tools to evaluate the genetic variability and to assess the mating system in <it>Arachis </it>species.</p>