Mangroves are more than just a tree as they are home to thousands of species, carbon absorbers and a natural coastal fortress against floods and storm surges. Hence, conservation planning and decision making for this valuable ecosystem must involve identification of priority conservation areas (PCAs) at species-specific dimensions. In the present study, we adopted an ensemble modelling approach for the distribution of two mangrove species (Rhizophora apiculata, Rhizophora mucronata) using high-resolution environmental and edaphic datasets, to identify the PCAs for future conservation. We also identified the key environmental variables shaping their distribution and precisely estimated the core distributional shift along the Indian coastline under changing climate scenario. The findings revealed that about 5844 km2 and 7846 km2 areas were identified as extremely suitable areas, which were distributed along Maharashtra coast and Kerala coast for R. mucronata and R. apiculata, respectively, in the current climate scenario. The distribution of R. apiculata was found to be mostly shaped by mean diurnal range and annual mean temperature, whereas the distribution of R. mucronata was primarily shaped by annual mean temperature and altitude. The highest range expansion of mangrove species occurred during middle Holocene due to high precipitation and sea-level rise and this finding is further supported by fossil pollen evidence. The suitable habitat range for R. apiculata is predicted to increase along Kerala coast under RCP2.6 scenario by 6.90% and 6.93% and under RCP8.5 scenario by 9.33% and 9.90% in the year 2050 and 2070, respectively, whereas the range for R. mucronata is getting reduced in the future climate scenario. Overall, our predictions reveal a steady migration of conducive mangrove habitat towards land or higher elevations due to relative sea level rise in future. These results would aid in planning a long-term species-specific conservation and management strategy for mangrove ecosystem along coastal India.