This study investigates the diversity and species composition of Acetes sp. from selected coastal waters of Terengganu, Malaysia. Morphological and molecular identification using mitochondrial DNA COI genes were employed to differentiate species and assess genetic variation. The results revealed the presence of two species, Acetes intermedius and newly discovered Acetes japonicus in Terengganu waters. A. intermedius was found in four locations, Pengkalan Gong Batu, Jeti Marang, Jeti Seberang Takir, and Rhu Muda, while A. japonicus was more prevalent in two locations, Pantai Air Tawar and Pengkalan Gong Batu. Genetic analysis identified 10 haplotypes in A. intermedius and 8 haplotypes in A. japonicus, indicating a relatively high level of genetic diversity within both species. These findings contribute to enhancing our knowledge of Acetes diversity along the eastern coast of Peninsular Malaysia, serving as a foundation for future investigations into the ecology and fisheries management of this significant genus.