The gDNA isolated from Korean cuttle fish (Sepia esculenta Hoyle) from Sockcho (SOCKCHO), Seocheon (SEOCHEON), Incheon (INCHEON) and Vietnamese cuttle fish (VIETNAM), were amplified by PCR. Here, the seven selected primers (BION-A07, BION-A09, BION-A11, BION-A20, BION-B04, BION-B06, and BION-B14) were used to generate the unique shared loci to each population and shared loci by the four cuttle fish populations. In this study, the primer BION-A11 detected 112 shared loci by the four populations, major and/or minor fragments of sizes 300 bp, 400 bp, 700 bp and 1,000 bp, respectively, which were identical in all samples. The dendrogram obtained by the seven primers indicates five genetic clusters: cluster 1 (SOCKCHO 01-SOCKCHO 07), cluster 2 (SEOCHEON 08-SEOCHEON 10), cluster 3 (SEOCHEON 11-SEOCHEON 14), cluster 4 (INCHEON 15-INCHEON 21), and cluster 5 (VIETNAM 22-VIETNAM 28). The shortest genetic distance that displayed significant molecular differences was between individuals 25 and 26 from the Vietnamese cuttle fish (0.025), while the longest genetic distance among the twenty-eight cuttle fishes that displayed significant molecular differences was between individuals SOCKCHO no. 02 and SEOCHEON no. 12 (0.640). Individual of Seocheon and Incheon cuttle populations was somewhat closely related to that of Vietnamese cuttle fish population. Even though it could not be affirmed by a single case, such a result seems to be closely connected that the Korean peninsula is subject to climate changes by global warming. In conclusion, our PCR analyses revealed a significant genetic distance among the four cuttle fish populations.