Abstract: We studied the morphological features of five stocks of the Metupenaeus ensis by using phenotypic parameter estimation analysis, cluster analysis, principal component analysis and discriminant analysis. Those stocks were Mindong stock(P.1), Yuedong stock(P.2), Yuexi stock(P.3), Beibuwan stock(P.4) and Hainandao stock(P.5). The cluster analysis reveals that P.1, P.2, P.3 and P.5 clustered to a large branch, while P.4 stock clustered to one independently. According to the results of principal component analysis, we find that the total contribution rate of the female stocks of the three main components was 65.70%; the cumulative contribution rate of the male stocks of the two main components was 67.24%; the determine contribution rates of the female stocks and male stocks were 61.48% and 71.66%, respectively. Significant morphological difference exists between Beibuwan stock(P.4) and the other four stocks.