The fatty acid composition of sakura shrimp muscle was used to determine the origin and estimate the dietary habits of the shrimp. The major fatty acids in sakura shrimp muscle were C16:0, C18:1n-9, C20:5n-3, and C22:6n-3. The discrimination rate between sakura shrimp from Suruga Bay and Taiwan was 90%. Consequently, it is considered possible to distinguish between shrimp from these locations based on the fatty acid composition. In addition, a positive correlation was found between the body weight and C18:1n-9/C18:1n-7 ratio of sakura shrimp from both Suruga Bay and Taiwan. Therefore, it is suggested that sakura shrimp may change their diet from herbivorous to carnivorous as they grow.