Abstract 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.