Our study involves Inter Simple Sequence Repeat markers to analyse genetic diversity of an undershrub, Gaultheria fragrantissima Wall. (Ericaceae) from two plant diversity hotspots in India, namely Western Ghats and Northeastern Himalayas. The plants from these two regions show no morphological differences but the total heterozygosity (H-T = 0.505) is high. Furthermore, the average heterozygosity of G. fragrantissima at WG (H-s = 0.433) is higher than that at NE region (H-s, = 0.231). Within population variance is higher (15.56 %) than among population variance (8.31 %) as seen in outcrossing plant species. Mantel's test shows a strong positive correlation between the genetic and geographic distances. The plants within WG show high gene flow, which may be enough to prevent genetic drift, however, the gene flow in NE population is very low.