Background and Objectives: In Iran considerable genetic resources of apple can be found in center, north and north east of the country and alongside the Caspian Sea. These genotypes have different phenotypes. In order to examine the levels of anthocyanin, phytochemicals, physical and chemical traits, the current experiment was designed and performed. Variations in size, skin and pulp color of the samples were found. The presence of genetic diversity led to more adaptation of plants to different environments and these enable researchers to selects superior genotypes. Since diversity in germplasm is backbone of breeding programs, the present research work was undertaken to evaluate different apple varieties using morphological and phytochemical characteristics by multivariate statistical methods. The experiment was conducted in 2016 as a completely randomized design with 12 native genotypes and 3 introduced ones with 3 replications. Materials and Methods: The fruits were collected from Kamal Shahr Horticulture Station of Karaj, affiliated to the Seed and Plant Improvement Institute. A total of 11 traits including weight, volume, density, firmness, acidity, total soluble solids and other characteristics were evaluated. The obtained data were subjected to analysis of variance using SAS (9. 1) software and Duncan's test was performed to mean comparisons. Results: Analysis of variance showed a meaningful difference among genotypes for all measured traits. According to the results, fruit weight varied from 161. 9 g in Fuji cultivar to 4. 25 g for Gol-ghermez cultivar. Acidity varied from 0. 88% for Gol-sefid to 0. 16% for Shahrood-10 genotype. The percentage of TSS varied from 19. 5% for Red delicious cultivar to 11. 5% for GH2 genotype and Golab-Kohanz cultivars. The highest positive correlation (0. 95) was observed between fruit weight and fruit volume. Based on the results of PCA, the cultivars were divided into three distinct groups, which were similar to our cluster analysis results. Conclusion: The results revealed that native Iranian apple varieties and genotypes are rich in genetic diversity and can play an important role in future apple breeding programs.