Abstract: Oujiang color common carp distributes in Zhejiang Province in southeast part of China,such as Lishui City,Longquan City,Qingtian country and Oujiang river basin.It has several color patterns,including whole red,red with scattered black spots,whole white,white with scattered black spots.Nowadays,several scientific researchers have car-ried out some works relevant to genetic diversity,genetic relationship in Cyprinus carpio var.color.However,we do not find any other studies on color-related molecular markers of Oujiang color common carp.Hence,it is necessary to ob-tain molecular makers for color correlative gene location and marker assisted selection(MAS).In this paper,Sequence Related Amplified Polymorphism(SRAP) technique was applied to identify the germplasm between "whole red"("WR") and "whole white"("WW") population.The specific SRAP fragment,namely SR2,7173bp(SR denote the first two letters of SRAP) from "WR" and "WW",was identified from the amplified products of 12 primer pairs screened from 88 SRAP primer pairs.After gel extraction,cloning and sequencing of this specific SRAP band,the sequence was submitted to dbGSS(data of Genome Sequence Survey).Blast analysis showed that this fragment had high similarity to functional genes of Danio rerio.Four primers(22 to 26 bases) were designed according to the sequence information.Then PCR amplification was carried out between "WR"and "WR"population.The experimental result also indicated that only SCAR-3(abbreviated SC-3,154bp) developed from SR2,7173bp(me2-em7) were "WR" specificity.Large samples ex-amination suggested that SC-3 could be positively amplified in "WR" population but not in "WW" population.Hence,SC-3 could be used a specific molecular marker for germplasm identification,which would provide a powerful,easy and rapid method for discrimination of different populations and genetic analysis.