In plant species, when clonal growth produces a patchy structure and flowering ramets are clustered, the amount of pollen contributing to reproductive success is often regulated by pollinator efficiency and geitonogamy. The spatial population structure may influence reproductive success. We examined the clonal structure, the spatial ramet distribution, and their combined effects on fruit set in a natural population of the insect-pollinated, self-incompatible clonal herb, Convallaria keiskei, in northern Japan. The number of shoots, flowers, and fruits in 1-m2 quadrats were counted at every 5 m grid point in an established 100 × 90-m study plot. From all the quadrats where shoots existed, leaf samples were collected for allozyme analysis. Using the two spatial parameters of flowering ramet densities and genotypes, we then constructed individual-based fruit-set models. A total of 236 quadrats contained shoots, and 135 contained flowering ramets, which indicated expanded distribution of this plant throughout the study plot, while shoots, flowers and fruits all showed clustering distributions. Allozyme analysis of 282 samples revealed 94 multilocus genotypes. The largest clone extended to more than 40 m, whereas 56 genotypes were detected in only one sample. Several large clones and many small clones were distributed close to each other. Fine-scale spatial modelling revealed that the neighbouring flower numbers of different genotypes, compared with local genet or flower diversity, more influenced fruit set, in which the range of the neighbour was 14.5 m. These findings indicate that the compatible pollen dispersed by insect pollinators has a significant effect on sexual reproduction, in this C. keiskei population. Consequently, the spatial structure, which includes both genet distribution and clonal expansion by ramets, had a significant effect on pollination success.