Physalis minima is abundant weed species in India commonly found in non-cropped and crop areas during Kharif season. Fruits of this weed species has been reported for high nutritional and medicinal values. Despite, no study has been made, so far, for their molecular diversity analysis. In the present study, genetic diversity was assessed among a total of 17 biotypes of P. minima and 1 intermediate biotype (which exhibits floral characteristics of both P. minima and P. peruviana). Using 42 random amplified polymorphic DNA (RAPD) markers, a total of 224 bands were amplified among all studied biotypes. The band size of amplified fragments ranged from 100 - 2200 base pairs (bp). Out of 224 bands amplified, 52 were found to be monomorphic (23.2%) and remaining 172 were polymorphic (78.8%). Average number of bands per primer were 5.33 while average number of polymorphic bands per primer were 4.09. Cluster analysis grouped all biotypes into two groups. This is the first report on molecular diversity analysis among Physalis minima biotypes.