The aim of this study was to assess the stem anatomical structure of divergent cherry germplasm and estimate genetic variation and heritability as well as hybrid enhancement for anatomical traits of cherry interspecific hybrids. Plant material included 18 cherry genotypes representing seven species and species hybrids. Analyses included detailed anatomical investigations of 1- and 2-year-old stems’ macro and micro cross-sectional characteristics, theoretical hydraulic conductance calculations, as well as estimations of genotypic and phenotypic variances, coefficients of variation, broad sense heritability, hybrid enhancement, and potence ratio. Average vessel lumen areas and percentages of vessels belonging to different size classes exhibited moderate to high heritability (more than 60%). In contrast, macro-anatomical characteristics—cambial-induced secondary thickening and production of secondary wood (xylem) and secondary cortex (phloem), appeared to be more environmentally sensitive. The high heritability of xylem vessel properties and low heritability of cross-sectional traits, along with previous knowledge regarding cambial-induced secondary thickening observed in the same germplasm, could be used to inform parentage choice for rootstock breeding crosses. The results support the hypothesis that xylem vessel size is primarily under genetic control and exhibits different degrees of dominance—partial (very close to better parent), full, and overdominance. It is presumed that the MSU rootstocks ‘Cass’ and ‘Clare’, followed by ‘Benzie’ and ‘Lake’ would have the greatest size-controlling effect on grafted cherry varieties, while Prunus maackii, the P. maackii × ‘Montmorency’ hybrid , and ‘Montmorency’ × ‘Colt’ hybrid would act as invigorating rootstocks. Our findings suggest that future hybrids between Prunus cerasus and Prunus fruticosa, the ‘weaker’ parental species characterized by smaller vessels, would result in rootstock candidates with better size-controlling effect, while crossings between P. fruticosa and Prunus mahaleb should have well-balanced vessel lumen areas and cambial activity, which is a prerequisite for successful adaptation to changing environmental conditions.