The peach (Prunus persica (L.) Batsch) and nectarine (P. persica var. nuscipersica Dippel) breeding program of the Agronomic Institute (IAC) began in the 1940s with the introduction of varieties from the United States. To date, 32 cultivars of peaches and four nectarine cultivars have been developed. In this study, we selected parental crosses by agronomic traits of fruits of 80 cultivars from the germplasm IAC-PRUNU. Therefore, a mixed model was adjusted considering a completely randomized design with five replications and six fruits per repetition. The evaluated traits were: fruit weight (FW), soluble solids (SS), titratable pH and citric acid content (CAC). The surface colour was assessed by factors hue and chroma angles. The narrow-sense heritability coefficient ranged from 0.01 (CAC-2012) to 0.95 (pH-2013), but, except for CAC-2012, all of these was intermediate or high. Based on the predicted breeding values, we detected statistically significant differences among genotypes for all traits. There was emphasis on cultivars 'IAC Douradao' and 'IAC Ouromel-2' and tree selections (IAC 2982-24, IAC 280-28 and IAC 280-29) as they showed higher frequencies of greater breeding value among cultivars in 2012; however, the cultivars with better frequencies were 'BRS Fascinio', 'Precoce de Itupeva', 'IAC Tropical-2' and 'FLA 81-17N'. We generated 497 seedlings (2012) and 345 seedlings (2013) from crosses and open pollination, which will be evaluated for agronomic traits. Overall, our results show the importance for conserving the germplasm IAC-PRUNU once it was possible to identify the genetic variability, which contributes to the future direction of crossings to obtain new cultivars.