Spain is the 15th largest apple (Malus ×domestica Borkh.) producer in the world with production depending mainly on foreign cultivars. During the 1970s, a germplasm bank of local cultivars was established in Galicia with the aim of preserving the local resources of northwestern Spain. A total of 408 accessions were studied using 89 morphological characters, with 15 corresponding to phenology, 46 to fruit, 7 to flowers, 11 to leaves, 6 to pests and 4 to diseases. Three variable isoenzymes, PGM E.C.184.108.40.206, PGI E.C.220.127.116.11 and EST E.C.18.104.22.168, were analyzed for 405 accessions and 27 commercial cultivars. The main objectives of this work were 1) to evaluate the inter- and intracultivar variability using morphological characters and isoenzymes, 2) to classify the accessions according to the main sources of variability, and 3) to identify repetitions in the germplasm bank. Principal component analysis (PCA) revealed six main sources of variability in the following order: size of fruit, color of skin, acidity, sweetness, harvest time, and attractiveness. The PCA analysis across 350 accessions produced 42 morphological groups. The 3 isoenzymes produced 190 genotype clusters. Combining morphological classification with the isoenzyme genotypes, we found 31 groups of synonyms involving 82 accessions and 8 more possible groups involving 17 accessions. This result allows the elimination of 53 repetitive accessions from the germplasm bank. Six commercial cultivars were identified as the progenitors of eighteen accessions: `Reineta Blanca' of seven, `Reina de Reinetas' of two, `Reineta de Caux' of eight and `Golden Delicious', `Golden 4187' or `Ozark Gold' of one each. Because inter- and intracultivar variability was high and names given by the growers were not reliable, the suggested selection strategy is to select individual clones among and within cultivars to exploit both the inter- and intracultivar genetic variability.