Vateria indica (Dipterocarpaceae) is an economically and ecologically important canopy tree endemic to the Western Ghats, India. The species has undergone extensive habitat loss and overexploitation and is therefore listed as ‘critically endangered’ on the 2012 IUCN Red List. We developed ten polymorphic microsatellite loci for V. indica. In addition, we confirm cross amplification and variation in two loci isolated from the closely related but geographically disjunct species Vateriopsis seychellarum, previously published by Finger et al. Conserv Genet Resour, 2 (S1):309–311, (2010). The twelve microsatellite primers screened on 48 adult samples of V. indica had 5–11 alleles per locus (mean of 8.5 per locus) with an average polymorphic information content of 0.64 across loci. Expected heterozygosity ranged from 0.44 to 0.84. These markers will enable us to quantify population genetic diversity in habitat fragments and to study fine scale spatial genetic structure and contemporary gene flow.