The Myristicaceae family is a primitive angiosperm family and is characterized by species that are highly endemic to the Western Ghats area of India. Myristica malabarica is confined to the evergreen forests of Western Ghats and Sri Lanka. In this paper we describe for the first time the development of eleven polymorhpic microsatellite markers for Myristica malabarica, which had 2–14 alleles per locus. These microsatellite markers could be used to study the population genetic structure of the species.