In this study, fifty six native apple genotypes from different geographical regions of Iran were evaluated based on 16 different biochemical and morphological characters using augment design. Analysis of variance showed significant difference between studied genotypes. Considering descriptive statistics, there was high level of genetic variation in this plant material. Regarding simple correlation between studied characters, fruit weight as one of the most important item, was positively and significantly correlated with fruit volume, leaf size and canopy axile. Principle component analysis revealed that the first seven principle components (PCs) were accounted 74.7% of the total variation. Cluster analysis using Ward method classified the 56 genotypes into four groups. As regards to clustering pattern, distribution of the cultivars was independent from their geographical distribution. The present study shows that Iranian apple genotypes possess high level of genetic variation that is useful for breeding.