This study uses the mitochondrial DNA control region to identify the genetic diversity and population structure of the marbled soles (Pleuronectes yokohamae) that inhabit Jinhae Bay and Yokji Island in the nearby sea and the adjacent waters of Namhae, Hansan Island, and Jaran Bay. Direct sequencing of the PCR products revealed 379 bp sequences with 83 variable nucleotide sites, defining a total of 91 haplotypes. The haplotype diversity was high, ranging from $0.917{pm}0.031$ to $0.983{pm}0.008$, and nucleotide diversity ranged from $0.015{pm}0.008$ to $0.024{pm}0.012$. In addition, 48 haplotypes (52.7%) were unique. Pairwise $F_{ST}$ values were very low, with the maximum value occurring between PYH (Hansan Island) and PJI (Jinhae Bay) ($F_{ST}$ = 0.011). Therefore, no significant genetic differentiation was evident between any pair of sampling localities.