Accessions of native fruits from ‘Arazá’ (Psidium cattleianum), ‘Guaviyú’ (Myrcianthes pungens) and ‘Guayabo del país’ (Acca sellowiana) were evaluated as part of a selection program to obtain commercial cultivars, with the aim to offer the growers new possibilities of local fruit crops and provide the consumers with food alternatives with recognized nutritional and nutraceutical properties. The objective of this work was to evaluate the physicochemical quality, the total phenolic content, vitamin C and total anthocyanins, and the relationship with the total antioxidant activity by DPPH and ORAC for different fruit genotypes. The methodologies for the determination of bioactive compounds and antioxidant capacity were validated on a microvolume scale, following the principles of “green chemistry”. The content of bioactive compounds differed significantly depending on the species and accession (p ? 0,05). The results obtained confirmed the nutritional properties and potential antioxidant capacity of the native fruits. The effect of agronomic and environmental variables on selected genotypes should be investigated to adjust commercial production technology in order to exploit the nutraceutical characteristics found.