Cydia pomonella L. is an important insect pest of pome fruits worldwide. We have isolated and characterized 17 microsatellite loci from the enriched genomic libraries constructed using a biotin/streptavidin capture protocol. Among these loci, 11 were scored polymorphic when 50 individuals from a laboratory population were screened. Their alleles numbered two to four, with the observed heterozygosity (HO) ranging from 0.114 to 0.404. Successful amplification was obtained for all these loci when the designed primers were tested, showing the promise of use in genetic mapping and population studies.