The 2004 Indian Ocean Tsunami and tectonic subsidence that ranged between 1.1 m and 2.85 m have severely impacted the mangrove habitats at the Nicobar Islands. The subsidence resulted in the loss of mangrove habitats; meanwhile, new inter-tidal habitats potential for mangrove colonization were also formed at the erstwhile terrestrial habitats. We assessed the impacts of the above mentioned large-scale natural disturbance on the mangrove habitats of Nicobar Islands and studied the initial patterns of mangrove succession. Surviving mangrove patches were observed at only three sites for the entire Nicobar Islands and the estimated mangrove cover loss is 97%, which is much higher than the previous reports. We report the presence of 20 mangrove species for the Nicobar Islands, which includes new distributional records and local extinctions after this major natural disturbance. The landward mangroves seem to be more vulnerable to such disturbances. The initial community structure of the successional mangroves is dominated by Rhizophora mucronata and Bruguiera gymnorhiza with a cumulative abundance of 70%. The community structure that included 3182 individual mangroves at the successional habitats showed a significant difference (P = 0.034) among the three islands groups (viz. Nothern, Central and Southern) in the Nicobar Islands. Habitat and species loss are inevitable with the high intensity of disturbance, in this case, tsunami and subsidence. But facilitating the mangrove regrowth at the potential habitats may be vital to restoring the functionality of the coastal system and the livelihood of local communities. Therefore, the outcome of our study is critical for the forest managers to regrow mangroves in the Nicobar Islands. Also, we suggest that a long-term monitoring of these sites is required to understand the overall long-term impacts of tsunami and subsidence on the mangrove habitats of Nicobar Islands.