Luculia gratissima (Wall.) Sweet (Rubiaceae) is a perennial shrub distributed in the southeast margin of the Tibetan Plateau in southwest China and adjacent region of Nepal and Myanmar. The plant is a distylous species with reciprocally placed stigmas and anthers in each floral morph. By using the Fast Isolation by Amplified Fragment Length Polymorphism (AFLP) of Sequences Containing (FIASCO) repeats protocol, 19 primer sets were identified in two wild populations. Of these primers, 10 displayed polymorphisms and nine were monomorphic. The number of alleles per locus ranged from two to five, values for observed and expected heterozygosities ranged from 0.000 to 1.000 and from 0.289 to 0.760, with averages of 0.303 and 0.555, respectively. These microsatellite loci will facilitate further studies on breeding system, gene flow patterns, and population structure of L. gratissima and its allied species.