Phyllanthus emblica and P. indofischeri, commonly known as the Indian gooseberry, are important nontimber forest product (NTFP) species widely distributed across the Indian subcontinent. The fruits of these species are rich in vitamin C and are used in the preparation of a number of herbal medicines for treating a wide range of disorders. Due to the increased demand, they have been harvested extensively and form a major source of income for the forest-dwelling communities living in southern India. There are limited studies to understand the impact of harvesting on the genetic structure of these species. In this study, 15 polymorphic microsatellite markers have been developed for P. emblica and were characterized by screening 20 individuals each of P. emblica and P. indofischeri. The number of alleles per locus ranged 2–9 for P. emblica and 2–11 for P. indofischeri. The observed and expected heterozygosity of P. emblica ranged 0–1 and 0.401–0.825, respectively. Similarly, the observed and expected heterozygosity of P. indofischeri ranged 0.5–1 and 0.366–0.842, respectively. Cross-amplification of the designed primers was assessed with seven related Phyllanthus species. The microsatellite markers developed can be used for studying the population genetic structure, gene flow and genetic diversity of P. emblica and P. indofischeri.