Morphological variations were analyzed for green turtles, Chelonia mydas, on the basis of 127 individuals captured in the coastal waters of Japan. They were explicitly divided into two groups by plastral coloration—the yellow type and the black type. To statistically assess the morphometric differences between these color types, analysis of covariance was performed for each of 28 external measurements using the standard straight-line carapace length (SCL) as the covariate. Results indicated that the yellow and black types significantly differ in ratios to SCL of distances from the nuchal notch to the outermost point of boundry between the 11th and the preceding (10th) marginals, and also to the boundary of the 11th marginal, last (fifth) vertebral, and last (fourth) pleural on both sides. Such morphometric covariations with plastral coloration in C. mydas sensu lato, as well as sympatric occurrences of the two color types in the Japanese waters, collectively support the validity of the black type as a distinct species, Chelonia agassizii.