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Morphometric and meristic analysis of ladyfish, Elops machnata, were used to discriminate stocks along the Southeast and Southwest coast estuaries of India. Morphometric and meristic analyses showed a similar pattern of differentiation between E. machnata stocks and revealed a clear discreteness of two groups, an East coast (Marakanam, Parangipettai and Muthupettai) population and a West coast (Cochin) population. Higher total length (TL) (28.00 ± 7.043 cm), fork length (FL) (89.27 ± 2.201% TL) and standard length (SL) (81.77 ± 2.582% TL) were recorded in Cochin population and they were significantly different from the other three populations. Meristic counts were relatively homogenous in all the studied populations. No significant variation was found in counts of dorsal fin ray (DFR), anal fin ray (AFR), pectoral fin ray (PFR) and pelvic fin ray (PLFR). The first and second components (PCA analysis) accounted for about 92.2% of variation in all the morphometric characters. Among them, pre pectoral length (PPL) and pre dorsal length (PDL) showed high loading values in PC1 in all four populations. The overall random assignment of individuals to their original group was higher in morphometric than in meristic analysis. Such a presumption could be authenticated henceforth with molecular markers. Hence, further studies, using molecular markers are still required to precisely evaluate the genetic structure of E. machnata along the Indian coast.