Abstract: The yellowfin seabream (Acanthopagrus latus) is an economically important fish species in China. Understanding its current genetic status provides a scientific basis for the conservation and utilization of its germplasm resources. This study analyzed the genetic diversity and differentiation of A. latus populations from Ningde, Xiamen, Zhangpu, Nan'ao Island, Zhanjiang, Haikou, and Beihai in China, based on mitochondrial COⅠ and 16S rRNA gene sequencing. The results revealed low genetic diversity in wild A. latus populations along the southeastern coast of China. For the COⅠ sequences (636 bp), 10 haplotypes were identified, with overall haplotype diversity (H_d) and nucleotide diversity (π) values of 0.510 and 0.00111, respectively. For the 16S rRNA sequences (408 bp), only 3 haplotypes were found, with overall H_d and π values of 0.078 and 0.00019, respectively. Analysis based on both sequences revealed low genetic differentiation among populations, with small genetic distances (COⅠ: D=0.00039−0.00177; 16S rRNA: D=0.00000−0.00066) and non-significant genetic differentiation coefficients F_st) (COⅠ: F_st =−0.03388−0.30000; 16S rRNA: F_st =−0.01818−0.30000). AMOVA analysis indicated that most genetic variation occurred within populations (COⅠ: F_st =0.03121; 16S rRNA: F_st =−0.00443). The NJ phylogenetic tree constructed using the Kimura-2-parameter distance method indicates that all individuals are intermingled, with no distinct clustering by geographic origin. In summary, the Chinese populations of A. latus exhibit no significant differentiation in COⅠ and 16S rRNA sequence and thus can be considered a single evolutionarily significant unit.