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The genetic assembly of Avicennia marina (Forsk.) Vierh, Avicenniaceae within and between the three natural mangrove forests of Kerala coast belonging to the districts of Kochi, Kozhikode and Kannur was investigated using Inter Simple Sequence Repeat (ISSR) markers to provide coherent scientific conservation practices. The ten selective ISSR primer combinations of 60 genotypes of Avicennia marina ensured a total of 171 bands of which 84.5% were polymorphic. Gene diversity index H varied from 0.142 Kochi to 0.195 Kozhikode. The mean gene diversity HS was 0.169 and the total gene diversity HT was 0.262 which showed a moderate level of genetic diversity in the studied population. The mangrove Avicennia marina populations showed large genetic difference GST = 0.3849, indicating that 38% of the total genetic diversity was among the populations and the rest 62% resides within the population. The gene flow estimates Nm = 0.79 shown that natural mangroves of Kerala are in the course of differentiation due to genetic drift. We investigated the genetic distinctiveness of taxonomically confusing species, Avicennia marina and Avicennia officinalis, and resulted in clear demarcation between the two. There is a significant correlation between dendrogram and PCoA designated that extensive distant spreading of seeds between populations of Avicennia marina is comparatively low. The genetic study contributed relatively high diversity and strong differentiation across the three eco-geographic locations. The best remedy to preserve coastal mangrove species like Avicennia marina is to plant the identical species in its respective habitat. Launch, on-site protection zones to safeguard the species and to decrease the impact of human activities would allow its habitats to increase in size through natural regeneration.