The traditional morphological methods implemented in mathematical statistic software,including clustering analysis,principal component analysis and discriminant analysis,have been widely used in dealing with morphological data in fishes.However,a series of molecular genetics software have also been developed coupling with development of modern molecular biology techniques.In this paper,in order to study the applicability of the molecular population genetics methods in analyzing fish morphological data,the morphological traits of nine mating combinations from a complete diallel cross of Xingguo red common carp(C.carpio var.singuonensis),Glass red common carp(C.carpio var.wananensis)and Purse red common carp(C.carpio var.wuyuanensis),were used to conduct comparative analysis of traditional morphological methods and molecular population genetics methods.The results showed that the same profiles of clustering analysis were found from the two kinds of methods.The principal component analysis indicated that the traditional morphological methods can better reflect the morphological variations among individuals,while the molecular population genetics methods can better reflect the morphological differences among populations.The discriminant analysis showed the similar discriminant accuracy of the two kinds of methods.Furthermore,the genetic clustering analysis results using software STRUCTURE illustrated the consistency of the two kinds of methods.Consequently,the study produced the same results from the traditional morphological methods and molecular population genetics methods in dealing with morphological data of red common carp.It is feasible to analyze morphological data of common carp using molecular population genetics methods.