Small populations of self-incompatible plants may be expected to be threatened by the limitation of compatible mating partners (i.e., S-Allee effect). However, few empirical studies have explicitly tested the hypothesis of mate limitation in small populations of self-incompatible plants. To do so, we studied wild pear (Pyrus pyraster), which possesses a gametophytic self-incompatibility system. We determined the S-genotypes in complete samplings of all adult trees from 3 populations using a PCR-RFLP approach. We identified a total of 26 different S-alleles, homologous to S-alleles of other woody Rosaceae. The functionality of S-alleles and their Mendelian inheritance were verified in artificial pollination experiments and investigations of pollen tube growth. The smallest population (N = 8) harbored 9 different S-alleles and showed a mate availability of 92.9%, whereas the 2 larger populations harbored 18 and 25 S-alleles and exhibited mate availabilities of 98.4% and 99.2%, respectively. Therefore, we conclude that even small populations of gametophytic self-incompatible plants may exhibit high diversity at the S-locus and are not immediately threatened owing to reduced mate availability.