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The tropical shads of the genus Tenualosa are important and high-value commercial clupeid fishes in the Indo-Pacific region. Although there is difficulty in accurately identifying tropical shads based solely on morphology, we successfully identified T. ilisha and T. toli from Peninsular Malaysia and Borneo, which were confirmed by an analysis using 16S ribosomal RNA gene sequences. We propose that accurate identifications of tropical shad species should always include molecular genetic analysis for precise species confirmation. There is an urgent need for studies on the ecology, population dynamics, and conservation of these species in Malaysia.