The hard tissues of squid can provide important information for species identification. In this study, we used statolith and beak to identify three squid species including Uroteuthis duvaucelii, Loliolus beka, and U. edulis in the South China Sea. Because of the highly overlapping habitat and similar body morphology of the three squid species, we explored four different ways to identify them, by using statolith, upper beak, lower beak and a combination of statolith and beak. An outline geometric morphometric method and stepwise discriminant analysis were used to evaluate the most suitable method for the identification. We found that the combination of statolith and beak had the highest cross validation rate that was 75.0%, 87.5% and 88.7% for U. duvaucelii, L. beka and U. edulis, respectively. Using two beaks had similar results and the lowest cross validation rate was 60.0%, 50.0%, and 73.7% for the upper beak, 46.9%, 58.5% and 75.3% for the lower beak of U. duvaucelii, L. beka and U. edulis, respectively. Analyzing with the statolith had moderate cross validation which was 72.2%, 80.0%, and 87.7% for U. duvaucelii, L. beka and U. edulis, respectively. From the results it is suggested when the entire body of a squid is available, a combination of statolith and beak should be used for the identification. When only one hard tissue is available, species identification can be subjected to large errors. The hard tissues of squid can provide important information for species identification. In this study, we used statolith and beak to identify three squid species including Uroteuthis duvaucelii, Loliolus beka, and U. edulis in the South China Sea. Because of the highly overlapping habitat and similar body morphology of the three squid species, we explored four different ways to identify them, by using statolith, upper beak, lower beak and a combination of statolith and beak. An outline geometric morphometric method and stepwise discriminant analysis were used to evaluate the We found that the combination of statolith and beak had the highest cross validation rate that was 75.0%, 87.5% and 88.7% for U. duvaucelii, L. beka and U. edulis, respectively. Using two beaks had similar results and the lowest cross validation rate was 60.0%, 50.0%, and 73.7% for the upper beak, 46.9%, 58.5% and 75.3% for the lower beak of U. duvaucelii, L. beka and U. respectively, respectively. The results of the statolith had moderate cross validation which was 72.2%, 80.0%, and 87.7% for U. duvaucelii, L. beka and U. edulis, respectively. From the results it is suggested when the entire body of a squid is available, a combination of statolith and beak should be used for the identification. When only one hard tissue is available, species identification can be subjected to large errors.