The distribution of Kogiid whales from the Indian Ocean waters, especially Indian waters are poorly known. It is extremely difficult to differentiate the two species (Kogia sima and K. breviceps) based on their morphological characteristics alone. Our study presents the first confirmed record of dwarf sperm whale Kogia sima from the Indian waters using morphological examinations, skull morphology and molecular identification. The study is based on the stranded animal found in the west coast of Agatti Island in Lakshadweep Archipelago belongs to the Indian EEZ. K. sima showed intra-species genetic variability which confirms the isolation of the species in oceans as the tropical nature of the species restricts its movement.