Abstract To clarify the taxonomic delimitation of the Lateolabrax japonicus complex, we conducted morphological and molecular analyses of 79 individuals collected from 10 localities in Korea. Assignment of individuals into three types (sea bass [SB], spotted sea bass [SSB] and intermediate sea bass [ISB]) was performed according to the presence/absence of black spots, and the distribution of black spots if present. Results of a canonical discriminant analysis showed that SB and ISB are closely related, but SSB is distinct from SB + ISB. Based on mitochondrial DNA COI sequences (507 bp), SB and ISB clustered together, and this cluster was distinct from that of SSB (d = 0.072–0.085). STRUCTURE analysis using six microsatellite markers showed the existence of two genetically differentiated groups (SB + ISB and SSB). However, ISB had a greater number of mixed individuals than SB and SSB, and was located distantly far from SB in the PCoA axis 2, implying restricted secondary contact within L. japonicus complex.