Genomic DNA isolated from two geographical populations of pond-smelt (Hypomesus nipponensis) was amplified for RAPD (randomly amplified polymorphic DNA) analysis. The populations were obtained from Chungju (CJ), in the inland area, and Dangjin (DJ), in the vicinity of the West Sea in Korea. Seven arbitrarily selected primers, OPB-06, OPB-10, OPB-13, OPB-17, OPC-09, OPC-17 and OPC-20, were used to generate the shared loci, polymorphic, and specific loci. Three hundred and eighty-three loci observed per primer were identified in the CJ population, and 287 were identified in the DJ population. Among them, 91 polymorphic loci or 23.8% were polymorphic in the CJ population, and 47 (16.4%) in the DJ population. The number of shared loci observed was 198 in the CJ population and 176 in the DJ population. Forty-four and 75 specific loci were detected in the CJ and DJ populations, respectively. Especially, 99 numbers of shared loci by the two populations, with an average of 14.1 per primer, were observed in the two pond-smelt populations. The average bandsharing value between the two geographical pond-smelt populations was $0.700{\pm}0.008$, ranging from 0.600 to 0.846. Compared separately, the bandsharing value of individuals within the CJ population was higher than that of the DJ population. The dendrogram obtained using the data from the seven primers indicated three genetic clusters: cluster 1, CJ 01, 02, 03, 04, 05, 06, 07, 08, 09, 10, and 11; cluster 2, DJ 01, 02, 03, 04, 05, 06, 07, 08, and 09; and cluster 3, DJ 10 and 11. The genetic distance between the two geographical populations ranged from 0.040 to 0.545. Thus, RAPD-PCR analysis revealed a significant genetic distance between the two pond-smelt populations.