Based on 8 morphological characters, three multivariation analysis methods (principal component analysis, discriminant analysis and cluster analysis) were used to comparably investigate the morphological variations of the first generation of three self-bred (TT,SS,YY) and seven corresponding hybrids (ST, TS, YT, TY, SF, TF and YF) in Penaeus monodon from four geographical populations. ANOVA analysis indicated that the first generation of different mating group showed some morphological variations except SF and TF. The principal component analysis of the first generation of Penaeus monodon yielded two principal components (PCs), which accounted for 72.54% of the total variation. In the first PC, which explained 48.15% of the total variance, the most important characters were numbered of the third pleon segment length (TSL), second pleon segment length (SSL), sixth pleon segment length (SISL) and carapace width (CW) of the shrimps. In the second PC (24.39%), expressed variables exclusively associated with the carapace length (CL) and body length (BL). Based on DFA evaluation, the proportion of individuals correctly classified into their original groups were very low. The cluster analysis indicated that there were most similar morphological characters among the stocks of ST, TS, TT and SF, TF, YF.