Preservation of the genetic diversity of sour cherry in Iran is imperative for the development of improved cultivars tailored to specific ecological conditions. Addressing gaps in research concerning ecological adaptation, resource management and international collaboration related to sour cherry genetic resources in Iran is essential. Bridging these research lacunae can facilitate the implementation of sustainable cultivation practices, optimize production systems and enhance the global utilization of sour cherry genetic diversity. A comprehensive analysis of the morphology and ultrastructure of pollen grains from ten native sour cherry genotypes in Iran was conducted over a two-year period using scanning electron microscopy (SEM). The examination revealed that all pollen grains were unipolar, radially symmetrical and tricolpate. The length and width of pollen grains varied among genotypes, with lengths ranging from 42.17 to 57.57 μm and widths from 20.28 to 28.13 μm. Furthermore, all genotypes exhibited prolate pollen grains, with differing colpus lengths. Examination of pollen exine revealed striate shapes with varying numbers of ridges, ranging from 18.5 to 8.5 furrows per 50 m2. The horizontal area of pollen grains varied from 333.28 to 1491.69 μm. Polar perspective analysis showed considerable variation in the distance between mesocolpium endpoints. Sour cherry displays significant genetic diversity in Iran, and the application of SEM has proven instrumental in characterizing this diversity. This understanding will aid in further breeding research aimed at enhancing sour cherry varieties and their adaptation to specific ecological conditions.