Two sympatric morphs (type A with a vertebral number of 25 and type B with a vertebral number of 24) of striped jack Pseudocaranx dentex (Bloch & Schneider) were analysed genetically. A part of the 16S-rRNA region of mtDNA was amplified with polymerase chain reaction for 24 specimens, and a restriction enzyme fragment polymorphism showed significant differences between the two types. While all specimens sampled in Ogasawara were identified as type B, about 90% of striped jack in Oita were type A and 10% were type B. Although the spawning areas of these two types are still unknown, significant genetic differences between the two sympatric morphs show that recruitment and migration patterns might differ from each other. The current system suggests the possibility that the juveniles of type B in Oita may migrate from the Ogasawara Islands.