One of the possibilities to improve the management of germplasm collections is to identify the redundancies that inevitably appear within and between collections. For this purpose, an accurate identification of the preserved accessions is an indispensable requisite. In terms of identification, traditional methods based on morphological and agronomic traits are less effective than molecular markers due to the fact that they can be highly influenced by environmental factors. The aim of this study was to quantify the duplication degree among three apple collections located in the Spanish and French Pyrenean region, using a common set of 14 SSR markers, as well as to assess the genetic relationships between the accessions held in the three collections. Only 17 genotypes (≈5% of the identified ones) were present in both Spanish and French collections. Two duplicates groups, nine (putative) synonyms and nine homonyms were identified. Remarkable differences in allelic variability and allelic frequencies distribution were found between the material preserved in Spanish and French collections, but the duplication and overlap highlighted the interest of coordinated international studies aiming at optimizing the management of germplasm collections.