A tropical shad of the genus Tenualosa is an important and high commercial value clupeid fish in the Indo-Pacific region. The tropical shads found in Peninsular Malaysia and Brunei Darussalam were identified using a morphological analysis, and the identification was further validated by an analysis of the shads’ 16S ribosomal RNA gene sequences. Although the difficulty of accurately identifying tropical shads solely on morphology was encountered, this study successfully identified T. ilisha and T. toli, which were confirmed by the molecular genetic analysis. The validation of occurrence of T. ilisha and T. toli calls for the urgent need for the studies of ecology, population dynamics and conservation of these commercially important species in Brunei Darussalam and Malaysia. The present study also proposes that accurate tropical shad species identification is difficult by morphological identification alone and thus should be supplemented with molecular genetic analysis for a precise species confirmation.