Population density,species richness and critical population parameters are crucial in determining the levels of gene diversity in dioecious species of the genus Calamus.The extent of intraspecific and intrageneric genetic variability in Calamus from the south West Ghats of India was studied using 26 microsatellite markers by sampling 227 individuals belonging to seven economically important species.The heterozygosity of microsatellite loci ranged from zero to 0.78.Average gene diversity within species was 0.13;in all species it was 0.18 and amongst species was 0.06.The Shannon Information Index was the lowest for Calamus metzianus (0.11),whereas it ranged from 0.16 to 0.26 for other species.The expected heterozygosity varied from 0.08 to 0.18.Calamus hookerianus and Calamu travancoricus showed the highest genetic differentiation (44％) revealed through Fst values,whereas the lowest (22％) was observed between Calamus gamblei and Calamu thwaitesii.Population structuring and phylogenetic analysis differentiated the seven species.Due to overexploitation and loss of rare alleles,small populations could lead to fertilization between closely related individuals,resulting in inbreeding and increasing the risk of extinction.This could be important for species such as C.metzianus where allelic polymorphism was 23％,whereas for all other species it was 38％ to 46％.Genetic diversity micro-hotspots were identified from the protected area network of the south and central West Ghats with highest observed heterozygosity.Four microhotspots from the Agasthyamalai Biosphere Reserve and the Pushpagiri Wildlife Sanctuary may be possible for long-term conservation programs.The findings of this study lay a strong foundation for strengthening protected area networks,especially areas with intermediate levels of disturbance.