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Not AvailableTraditionally, fish species identification is based on morphological characters, yet, in many cases it is difficult to establish identity as in the case of seahorses which lack key species-diagnostic morphological features. The spotted or yellow seahorse - Hippocampus kuda has a complex identity and the samples collected from the east and west coasts of India were analyzed for the species identification and phylogenetic relationship, based on partial sequence information of mitochondrial genes - 16S rRNA and Cytochrome Oxidase subunit I (COI). Estimates of genetic divergence with both 16S rRNA and COI genes, when compared with the sequence divergence values of H. kuda from other continents (as obtained from NCBI accessions) were sufficient enough to discriminate individuals of the same species from Indian waters. Pair-wise fST values using AMOVA indicated significant levels of genetic differentiation of H. kuda populations among east coast, Kerala and Konkan populations; however, no significant genetic partitioning was observed between the Palk Bay and Gulf of Mannar populations.Not Availabl