<p>Accurate species identification and labeling in inspection are predominantly hindered in semi-processed shellfish due to a lack of external morphological features. Therefore, this study aimed to compare three primer sets in amplifying the mitochondrial cytochrome c oxidase subunit I (COI) gene to identify species through sequence analysis. A total of 147 imported shellfish (clams, mussels, and scallops) were collected from 2021 to 2023. The polymerase chain reaction (PCR) was performed using three primer sets for each sample, followed by Sanger sequencing and phylogenetic analyses for species identification. Universal primers exhibited the highest performance in clams and mussels, while Matsumoto primers were the most effective for scallops. In total, eight species of clams, four species of mussels, and two species of scallops were identified. Some species or exporting countries were found not to match the product label. Overall, COI-based sequence analysis can be used for reliable molecular species identification and to prevent mislabeling in seafood inspection systems.</p> Graphical Abstract <p></p>