Iran, with a long history of apricot cultivation is one of the most important apricot producers in the world. Centuries of sexual reproduction via seed, have developed many divergent variations of apricots in Iran. However, unfortunately there is no comprehensive report available concerning its diversity and genetic make-up. In this study, 39 Iranian apricot cultivars as well as accessions, native to Iran, were evaluated using morphological and RAPD molecular markers. Total Soluble Solids (TSS), Titrable Acidity (TA), kernel weight, fruit flesh weight as well as fruit weight exhibited high diversity coefficients, making it possible to select for desirable characters in breeding programs. In addition, factor analysis was performed to determine the number of the main factors. A 79.52% level of total variance was explained by the first six factors for morphological discrimination, the first independent factors of which included fruit size (24%), pit (16%) and flavor (14.5%). Cluster analysis of morphological traits led to a separation of cultivars according to their fruit size, ripening season as well as characteristics related to fruit taste. According to the RAPD, the highest genetic similarity was observed between ‘Noori-Dirras’ and ‘Noori-Pishras’ (0.95) while the lowest between ‘Tanasgol’ and ‘Shahrood-48’ (0.3). In the cluster analysis, at similarity distance of 65%, cultivars were placed in six main groups, in agreement with some other results obtained from morphological analysis and from the geographical origins of accessions.