Pears (Pyrus spp.) mainly are divided into two main groups of Asian and European species with a wide diversity or similarity in fruit and morphological traits. In this study, flow cytometry was performed to evaluate the genome size of 37 cultivars and genotypes of Asian, European, and Iranian indigenous pears. Besides, the relationship between cytological and morphological traits was investigated for the first time. Morphological traits were measured based on the International Union for the Protection of New Varieties of Plants (UPOV) descriptor. There were positive relationships between genome size, the fruit pedicel length, and the length to fruit diameter ratio. Although, as the genome size was increased, the fruit diameter and size were decreased. Increasing 1.6 pg of the genome size causes a reduction of one cm in the pear fruit diameter. Moreover, with a larger genome size by 1.1 pg, there was an increase in fruit pedicel by one cm. The obtained results revealed that most of the Iranian native genotypes were similar in shape to European pears, but some of them were also oriented to Asian pear cultivars. Most studied cultivars originated between different regions were diploid (2n = 34) and their genome size varied between 0.99 and 1.99 pg. The average genome size of European and Iranian pears was 1.29 pg and Asian’s was 1.32 pg. The principal component analysis (PCA) result showed that the Asian and European genotypes were distinctly separated. Also, according to the cluster analysis, the indigenous cultivars of Iran can be located in the European pear group species. There was a relationship between the East Asian and European pear origins because of the possible gene flow between two major pear culture regions in the past. In general, Iran can be considered as an important region and pathway of gene flow transfer and a rich center of genetic variation of pears. Therefore, this study provided essential information and a useful tool for genetic diversity or similarity assessment of pears through genome size and some morphological traits prediction. Further research on wider fruit tree species in the different fruit-growing regions of the world will warrant the use of genome size as a novel prediction tool for the important morphological traits with specific commercial breeding objectives.