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Investigating spatial variation in the relative importance of sexual reproduction and clonal propagation is critical to obtain more accurate estimates of future effective population sizes and genetic diversity, as well as to identify ecological correlates of clonality. We combined a stratified sampling scheme with microsatellite genetic analyses to estimate variation in the proportion of sexual versus clonal recruits among saplings in five populations of the tree Pyrus bourgaeana. Using a likelihood framework, we identified clones among the genotypes analysed and examined variation among populations regarding the proportion of saplings coming from clonal propagation. We also examined the relationship between the relative abundance of clonal shoots across the studied populations and their herbivory levels. Our results revealed that one third of the saplings examined (N = 225 saplings) had a probability above 0.9 of being clones of nearby (<10 m) trees, with the ratio between clonal propagation and sexual recruitment varying up to eight-fold among populations. A small portion of these putative clonal shoots reached sexual maturity. Relative abundance of clonal shoots did not significantly relate to the herbivory by ungulates. Our results call into question optimistic expectations of previous studies reporting sufficient levels of recruitment under parental trees without animal seed dispersal services. Nevertheless, given that some of these clonal shoots reach sexual maturity, clonal propagation can ultimately facilitate the long-term persistence of populations during adverse periods (e.g. environmental stress, impoverished pollinator communities, seed dispersal limitation).