Mango (Mangifera indica L.), an edible fruit, is one of the main agricultural products in many tropical regions. Mango varieties differ in not only fruit shape but also aroma, which is an important characteristic. Although the fruit has many uses, the seeds are discarded as waste. Therefore, this study aimed to estimate the fatty acid content of seed oil of mangoes from different cultivation areas (Miyazaki, Japan, and Taiwan), and to evaluate their application in cosmetics. Five fatty acids were identified in the mango seed oil. Oleic acid and stearic acid were the principal components of mango seed oil obtained from Miyazaki (46.1% and 39.8%, respectively) and Taiwan (43.7% and 40.1%, respectively). As a cosmetic ingredient, mango seed oil showed good deodorizing effect on both 2-nonenal and isovaleric acid. The results indicated the potential applications of mango seed oil in the cosmetic industry.