The aim of this study was to examine the dimensions and surface morphology of pollen grains of some sweet and sour cherry genotypes through scanning electron microscopy (SEM) as an additional alternative identification tool. In vitro pollen germination and pollen tube length as indicators of their viability were determined as well. Observations were carried on 10 sweet cherry (Prunus avium L.) and 7 sour cherry (Prunus cerasus L.) genotypes. All genotypes had prolate, tricolpate pollen grains, and striate exine ornamentation, with more parallel longitudinal ridges. Significant differences among genotypes within species and between species were found for most pollen grain characteristics and exine ornamentation. In both sweet and sour cherry the largest variability was recorded for colpus length (CV = 15.0% and 12.9%, respectively). For sweet cherry genotypes, in vitro pollen germination and pollen tube length ranged between 1.4% to 51.5% and 360.4 to 669.3 μm respectively, while for sour cherries they ranged from 15.5% to 37.0% and 96.3 to 960.2 μm, respectively. The results of the correlation analysis showed that in vitro pollen germination correlated positively with pollen length/pollen width (L/W) ratio (r = .640) and furrow width (r = .588), and negatively with the number of ridges (r = -.517), while pollen tube length was not significantly correlated with any of the studied characteristics. Principal component analysis (PCA) revealed that pollen length, pollen width, L/W ratio, colpus length, mesocolpium width, and ridge width are relevant tools to discriminate among the studied genotypes. The measurements made on pollen grains did not reveal individually big differences, but when all features were considered together, the pollen of each genotype exhibited a unique pattern. The distribution on the scatter plot showed considerable variation among sweet and sour cherry genotypes based on pollen morphological characteristics, which led to their distribution into two separate groups. This demonstrates the ability to distinguish cherry species based on pollen morphological characteristics determined by SEM. To improve discriminative ability for genotypes within species combination between pollen ultrastructural analysis, morphological and molecular markers is desirable, in subsequent work. RESEARCH HIGHLIGHTS: Significant differences in pollen characteristics between sweet and sour cherry. Significance of pollen morphology in taxonomic differentiation. Significance of SEM studies for the taxonomic identification.