Lychnophora ericoides is an endangered species, endemic to cerrado rupestre. Herein we report the development and characterization of 13 polymorphic microsatellite loci for the species, using enriched genomic library. Number of alleles per locus and expected heterozygosity ranged from 06 to 13 and 0.696 to 0.894, respectively. The high combined probability of genetic identity (2.69 × 10−17) and probability of paternity exclusion (0.9999) showed that multilocus genotypes are likely to be unique and will allow detailed parentage studies in natural populations of L. ericoides.