The genetic diversity of cultured and wild silver pomfret (Pampus argenteus) populations was analyzed based on mtD-loop and COI gene. The results showed that the average A, T, C and G contents in D-loop were 40.00%, 30.55%, 16.75% and 12.70%, respectively, and the contents of A + T were 70.55%, higher than those of G + C. In the COI gene, the average A, T, C and G contents in Dloop gene were 25.85%, 33.90%, 21.30% and 18.85%, respectively, and the contents of A + T were 59.75%, also higher than those of G + C. The total variable sites, number of haplotypes (h), haplotype diversity (Hd), nucleotide diversity (π) and mean pairwise nucleotide differences (k) of two populations based on D-loop were 19, 15, 0.895, 0.007 and 2.505, respectively. The same parameters based on COI gene were 33, 17, 0.713, 0.004 and 2.239, respectively. Based on mtD-loop and COI gene, the genetic diversity of cultured population was lower than that of wild population. The Hd of cultured population based on mtD-loop and COI gene were 0.562 and 0.571, respectively. And the Hd of wild population were 0.891 and 0.801, respectively. The AMOVA analysis based on D-loop showed that the significant genetic divergence existed in cultured and wild populations, while there was no significant genetic divergence when it was analyzed based on COI gene. In conclusion, both D-loop and COI gene were effective molecular markers for analyzing the genetic diversity of silver pomfret population, while the sensitivity of D-loop in detecting the genetic diversity among populations was higher than that of COI gene.