This study identified 260 lanternfish larvae specimens belonging to 20 species from 12 genera, which were obtained from 544 samples of the Ninety East Ridge waters in the Indian Ocean using the COI DNA barcoding. Among the samples, the intra-specific genetic distances ranged from 0% to 2.99%, while inter-specific genetic distances ranged from 1.88% to 25.71%. With the exception of Notolychnus valdiviae, the maximum intra-specific genetic distances were lower than the minimum inter-specific genetic distances for all species. The haplotypes of nine species were analyzed, revealing significant differences in the number, structure, and spatial distribution patterns. Notably, Ceratoscopelus warmingii and Notolychnus valdiviae displayed a significant north-south divergence pattern. The results indicated that seamount topography may influence the gene flow and horizontal distribution patterns of some lanternfish species, as shown by the distribution patterns of different populations of some species.