The present study was conducted to identify and characterize two bivalve species, Sinanodonta woodiana and Corbicula fluminea, collected from Thi-Qar Province, southern Iraq, based on sequence analysis of the mitochondrial cytochrome oxidase subunit 1 (COX1) gene. Samples of S. woodiana and C. fluminea were collected from the Al-Gharraf River in Thi-Qar Province from October 2023 to September 2024. Genomic DNA was extracted from 10 samples—five individuals each of S. woodiana and C. fluminea. The mitochondrial COX1 gene was amplified by PCR, and the amplicons (710 bp) were subsequently sequenced. Sequence analysis revealed that the identified S. woodiana sequences showed 99–100% similarity compared to international samples available in the NCBI database. Two COX1 sequences of S. woodiana obtained in this study have been deposited in GenBank with accession numbers LC833751.1 and LC833752.1, along with three sequences of C. fluminea (LC833753.1, LC833754.1, and LC833755.1). Phylogenetic analysis placed the Iraqi specimens of both species in clusters with their counterparts from various global regions. The findings of this study also highlight genetic variations within these two bivalve species.