The authors have investigated three species of Clupeidae such as herring, Korean anchovy and large-eyed herring, belonging to the order Clupeiformes. The fish is also indigenous to some parts of the southern regions of the West Sea. Fishes are the most popular marine products in Korea because of their taste and nutritional value, and Koreans consume them in large quantities. Especially, Korean anchovy and large-eyed herring are widely distributed in the entirety of brackish-water habitats and seawater areas of the West Sea in the Korean Peninsula, as well as in several areas in China. However, in spite of their economic and scientific consequences, a little information currently exist regarding the physiological and ecological levels only of crab species in Korea. During the last two decades, environmental contamination and various environmental disruptions by industries and city sewage, have threatened the coastal fisheries, and then reduction of individual number of this fish is an increasing trend in the 2000s. This study attempt is to elucidate the genetic distances within and between herring, Korean anchovy and large-eyed herring population from the West Sea. Three species of herring (C. pallasii), Korean anchovy (C. nasus) and large-eyed herring (H. zunashi) were obtained in close vicinity to the West Sea in Korea. Three species of fish muscle was collected in sterile tubes, placed on ice immediately, and stored under refrigeration until needed. Genomic DNA was extracted and purified under the conditions described previously (Yoon and Kim, 2004). The degree of variability was calculated by use of the Dice coefficient (F), which is given by the formula: F = 2nab / (na+nb), where nab is the number of bands shared between the samples a and b, na is the total number of bands for sample a and nb is the total number of bands for sample b (Jeffreys and Morton, 1987; Yoke-Kqueen and Radu, 2006). Euclidean genetic distances within-and between-species were also calculated by complete linkage method with the help of the hierarchical dendrogram program Systat version 10. The genomic DNA isolated from herring (C. pallasii), Korean anchovy (C. nasus) and large-eyed herring (H. zunashi) in the West Sea, were amplified several times by PCR reaction. The dendrogram obtained by the seven primers indicates three genetic clusters as shown in Fig. 1. The hierarchical dendrogram indicates three main branches: cluster 1 (PALLASII 01, 02, 03, 04, 06 and 07), cluster 2 (NASUS 08, 09, 10 and 11), and cluster 3 (NASUS 12, 13 and 14, ZUNASHI 15, 16, 17, 18, 19, 20 and 21, PALLASII 05). The genetic distance among the three fish species ranged from 0.018 to 0.318. In three fish population, the shortest genetic distance displaying significant molecular difference was between individual PALLASII no. 03 and PALLASII no. 02 (0.018). Ultimately, individual no. 05 of the PALLASII herring was most distantly related to PALLASII no. 06 (genetic distance = 0.318). From what has been said above, the potential of this PCR analysis to identify diagnostic markers for the identification of three fish populations has been demonstrated. Generally speaking, this PCR analysis method has been applied to identify specific markers particular to line, species and geographical population, as well as genetic diversity/polymorphism in diverse species of organisms (McCormack et al. 2000; Yoon and Kim 2003).