A dinucleotide microsatellite-enriched genomic library was obtained from Carica papaya L. Sixty-nine microsatellites were evaluated on three genotypes of C. papaya and seven species of the neighbour genus Vasconcellea. Among them, 45 markers were characterized on a sample of 29 accessions of C. papaya from the Caribbean region and 11 accessions of Vasconcellea from the Andes of Colombia and Ecuador. Twenty-four gave polymorphism in C. papaya and only four among the seven species of Vasconcellea, confirming the divergence between both genera.