Abstract: Papaya seeds have natural barriers (phenolic compounds, seed structure and genetic factors) that make their germination difficult. And the use of seeds is the main means of propagating the species, whether for commercial cultivation, maintenance of germplasm or selection of genetic materials. Thus, the use of seeds with physiological quality (germination, normal seedlings and germination speed) is fundamental to the production of vigorous plants. However, few studies have been developed with the aim of evaluating and improving seed quality. From this perspective, the study aims to evaluate the quality of seeds in genetic materials widely used to obtain new genotypes, in order to identify superior materials and possible crosses between those that have high physiological seed quality. For this purpose, 44 genotypes were analyzed by molecular characterization, via microsatellite markers (observed and expected heterozygosity, number of alleles, information index, fixation index, inbreeding coefficient, genetic structure and genetic dissimilarity via UPGMA grouping), as well as determining physiological quality of the seed (germination speed index, percentage of germination and abnormal seedlings). Among the genotypes, 10 have germination above 60%, a high rate of germination speed and a low percentage of abnormal seedlings, and can be used in crosses to improve seed quality. The dissimilarity analysis was able to highlight the dissimilarity between the accessions of the Solo and Formosa groups. The use of the dissimilarity coefficient and the number of shared alleles made it possible to identify 18 possible crosses promising to improve the quality of papaya seeds.