Avicennia marina is a true mangrove species dominated in most of the mangrove formations in India. These forests are considered as the most productive ecosystems on the planet. Mangroves play significant role in Biodiversity management and climatic changes. These ecosystems have several morphological as well as physiological adaptations to withstand the extreme environmental conditions. However due to anthropogenic activities and rapid changes in climate these ecosystems are facing severe threat for the last few decades. In order to conserve these mangrove populations and for implementing effective conservation strategies knowledge about the population genetic structure and genetic information is very crucial. The whole genome data of A. marina provided will be very significant in understanding the genetic makeup of the species and to infer the population genetic structure. This Data represent the first whole genome sequence of A. marina from south Indian population. In fact the data can be used to identify specific regions in the genome corresponds to the adaptive mechanisms exhibited by the species which is unknown.