Abstract Selection of superior genotypes based on the simultaneous responses to different characteristics is a fundamental strategy in plant breeding. This study aimed to compare the efficiency of four selection index constructed using phenotypic and genotypic values in a segregating population of the cultivar Rubi Incaper 511. Eight morpho-agronomic variates and the severity of black-spot and phoma-spot were evaluated under field conditions. The classical selection index were calculated based on non-standardized phenotypic means (NSM), standardized means (SM), and genotypic values predicted by REML/BLUP (GVP), using predetermined economic weights. Additionally, the rank sum (RS) was obtained on the basis of the classification of individuals in these three selection index. For ten characteristics, the selected individuals showed a higher mean than did the original population. The best selection differential values were obtained by SM, however, the highest degree of coincidence among the selected individuals was obtained between GVP and RS (80%). The index used were efficient at selecting individuals with higher soluble solids and lower diseases severity evaluated. Therefore, for the papaya breeding programs, different selection index need to be evaluated to maximize genetic gain.