Medicinal plants are popular and widely used as a major source of herbal drugs and pharmaceutical compounds. Ever-growing demands make medicinal plants faced to several problems including efficacy and safety to meet business requirements, conservation, and artificially assisted breeding. As a powerful molecular tool, microsatellites offer the great potentials for various purposes in plants. This review provides a scenario of microsatellites in medicinal plants including development from genomic or expressed sequence tag libraries, cross-species transferability, genotyping, and potential applications. We emphasized on the authentication of medicinal plants by microsatellite markers.