Summary The population of apple, Malus pumila Mill., indigenous to northwest Spain shows a wide range of ripening periods and fruit quality and is an unexploited resource for breeding programmes. The main purpose of this study was to fingerprint these accessions and to construct a molecular database including the cultivars commonly grown in Spain. A total of 77 indigenous and 26 international accessions were analysed using ten microsatellite [simple sequence repeat (SSR)] markers. Some of the main morphological and agronomic characteristics, such as fruit weight, colour, shape, sweetness in ºBrix, flavour type according to content of malic and tannic acids, and harvest time were recorded. The 77 Spanish cultivars showed a unique fingerprint. We propose to preserve these 77 genetically different cultivars in our Germplasm Bank, and recommend that 31 of them should be considered for a core collection to maintain all the diversity recorded. Some 29% of the cultivars showed three alleles at several loci and were confirmed, cytometrically, as triploids. These tended to produce larger fruit (15% by weight) than diploids. The use of ten polymorphic microsatellite markers provided a useful technique for fingerprinting apple cultivars in the Spanish germplasm resource and for indicating triploids. The fingerprints indicated that the famous triploid Dutch cultivar ‘Belle de Boskoop’ may be derived from an unreduced gamete of ‘Reinette de Caux’.