Although scute pattern abnormalities in sea turtle species are considered to be strongly correlated with survival rate, there is little information available regarding these abnormalities and the primary cause for their development is unclear. For the conservation of sea turtle species, accumulating basic knowledge of scute pattern abnormalities is a fundamental step towards a better understanding of the causes of these abnormalities. In the present study, we counted vertebral and costal scutes from adults hunted for food (male and female) (n = 899), nesting females (n = 155), and hatchlings (n = 44,537) of the green sea turtle (Chelonia mydas) from the Ogasawara Archipelago, Japan. We found that the frequency of turtles with non-modal scute patterns was significantly greater in adult females than that in adult males (P = 0.02). Since females are produced by warmer incubation temperatures, and the period of sex determination coincides with the period of scute pattern determination, high incubation temperatures may be responsible for the induction of scute pattern abnormalities. Moreover, females with non-modal scute patterns produced a higher frequency of hatchlings with non-modal scute patterns than females with modal scute patterns (P < 0.01), indicating that scute abnormality may be heritable. For conservation of this species, our results suggest that decrease of the incubation temperature by cooling methods, such as provision of shade, may minimize the frequency of non-modal scute patterns, with consideration for the natural sex ratio.