Phenotypic quantitative traits are the main basis for fish classification and germplasm characterization, and phenotypic traits contain rich genetic information. This study analysed 14 phenotypical quantitative traits of three biological populations of groupers:Kelp grouper(♀) Epinehelus moara, Giant grouper(♂) E.lanceolatus, and their hydrides "Yunlong grouper" by using multiple comparisons, hybridization coefficient comparison, discriminant analysis and principal component analysis methods.The results showed that the phenotype similarity of the "Yunlong grouper" was 27.27% with that of the female Kelp grouper, and it was 54.54% with that of the male Giant grouper. The similarity rate between the Kelp grouper and the Giant grouper was 54.54%.The average hybridization coefficient of 14 traits was 76.01, which indicated that the hybrid progeny on the phenotypic traits was biased towards male parent. The seven major quantitative traits of the hybrid progeny and parents, including body length/tail handle length, head length/eye spacing, body length/head length, tail handle length/tail handle width, body length/tail handle width, abdominal fins, dorsal fins soft fins, were further analyzed by discriminant analysis and principal component analysis. By comparing the typical discriminant function(F₁, F₂) and the discriminant function(Y₁, Y₂, Y₃) which can distinguish the above three biological groups, the discriminant accuracy rate reached 98.85% on average and can classify the 3 biological groups in two-dimensional space.Principal component analysis showed that the total variance of the first three principal components of the total variance accumulated contribution rate was 62.891%, fitting the three representative characters of principal component function (P₁, P₂, P₃), indicating that the three biological groups could be clearly distinguished in three-dimensional space by using principal components.This study provides a scientific basis for the identification of the germplasm of the Kelp grouper, Giant grouper and hybrids progeny "Yunlong grouper".