Red guava (Psidium cattleyanum Sabine) and guabiju (Myrcianthes pungens (O. Berg) D. Legrand) are small fruits that are native to southern Brazil. This study evaluated the physicochemical composition, antioxidant activity and functional compounds of both fruits. Red guava exhibited a large amount of dietary fibre. Guabiju showed more antioxidant activity, had a higher anthocyanin content and had a higher carotenoid content. In the guabiju fruit, β-carotene represented 40.4% of the total carotenoids, and malvidin 3-glycoside represented 60% of the total anthocyanin content. β-Cryptoxanthin was the predominant carotenoid in red guava, representing 44.8% of the total carotenoids; cyanidin 3-glycoside was the predominant anthocyanin, representing 51.7% of the total anthocyanins. These native fruits could represent an alternative to traditionally consumed fruits, and then, the characterisation of bioactive compounds of fruits such as red guava and guabiju represents important information to the consumers who looking for a healthy diet.