Mitochondrial phylogeography reveals high haplotype diversity and unique genetic lineage in Indian dugongs (Dugong dugon)

India plays a significant role in dugong conservation by having the largest population within South Asia. The status of dugongs in India is largely unknown due to a paucity of reliable ecological data. This study generated mitochondrial control region sequences from ~10% of dugong individuals from existing populations within India. Furthermore, data generated in this study were compared with the global data to assess genetic lineages, population structure, and genetic diversity of Indian populations. Multiple analyses suggest that the Indian dugong populations are part of a single genetic cluster, comprising South Asia, North‐west Indian Ocean, and South‐west Indian Ocean populations. Despite small population size, they retain high genetic diversity with unique mitochondrial DNA haplotypes within South Asia. Within India, novel haplotypes are observed from all dugong habitats sampled, with overall high haplotype diversity (0.85 ± 0.04) but low nucleotide diversity (0.005 ± 0.001). Indian populations exhibit genetic differentiation with higher within‐population variance (63.41%) than among populations (36.59%). Two of the haplotypes observed in India are shared with Sri Lanka, implying genetic connectivity between these populations. The genetic data from Indian dugong populations provide critical insights into the identification of dugong corridors and important dugong conservation zones in India. We suggest site‐specific interventions, including the creation of new marine protected areas and boundary reorganization and expansion of other existing protected areas, to ensure population connectivity. In addition, simultaneous efforts towards seagrass meadow restoration, reduction of dugong mortalities, and community participation in dugong conservation are recommended for population recovery of this threatened marine herbivore.