A microsatellite-enriched library was constructed in the Andean root crop arracacha (Arracacia xanthorriza B). Of 18 loci tested, 14 were found to be polymorphic after screening for diversity in different cultivars and related wild forms. Allelic diversity in the crop was low but the transferability of the primers to closely related wild forms was good. The loci reported here are the first genetic markers to be published for this species and will be useful for future germplasm characterization and studies of genetic diversity.