The invention provides a carp germplasm resource identification method, and relates to a fish germplasm resource identification method. The invention provides a method for accurately identifying fish germplasm at low coat without depending on a phenotypic character. The method comprises the identification steps that 1, the individual genome DNA (deoxyribonucleic acid) of a carp to be identified is extracted; 2, SNP sites relevant to carp anti-herpes virus are used for comparison, so that a carp individual germplasm resource can be identified. In various disease resistant genes, mononucleotide polymorphism markers relevant to the carp anti-herpes virus are selected for germplasm identification, so that the method has the advantages that the selected SNP sites are few; the method is relatively simple; the cost is low; the influence by external conditions such as environment is avoided; the accuracy is high.