The purpose of this research was to evaluate the plastid trnH-psbA spacer and the matK coding sequence as possible markers for the molecular characterization in two accessions of quince (C. oblonga), one from Argentina and the other one from Costa Rica. The study was carried out at Center for Biotechnology Research (CIB in Spanish) of the Technological Institute of Costa Rica (ITCR, in Spanish) during 2014. Amplified products were analyzed using MEGA v6.0 software to calculate genetic distances using the Tamura-Nei model.The results showed that the matK sequence presented the highest percentage of variable sites and the highest intraspecific distance, suggesting the presence of polymorphisms between the two accessions. On the other hand, the trnH-psbA spacer for quince had a low ability to discriminate because, at intraspecific level, this locus showed less differences.