Based on 50 samples of Sepia pharaonic and 100 samples of Sepia kobiensis collected in the East China Sea in 2015, the paper studied the species identification between Sepia pharaonic and Sepia kobiensis by principal component analysis and stepwise discriminate analysis. Results showed that there were highly significant differences in the 12 morphological parameters of beak between two species except LHL/ML. There were not significant differences between male and female in both species. The total successful discrimination rate for Sepia pharaonic and Sepia kobiensis by stepwise discriminate analysis was 94.8%. The total successful discrimination rate for Sepia pharaonic and Sepia kobiensis based on the result of principal component analysis was 83.6%. The total successful discrimination rate for male Sepia pharaonic and male Sepia kobiensis was 93.8%. The total successful discrimination rate for female Sepia pharaonic and female Sepia kobiensis attained 96.6%.