Dwarf bamboos are monocarpic and take several decades to flower. It is a rare occasion to have a chance to get sound seeds of dwarf bamboos. We have been observing a small-scale flowering of dwarf bamboo species every year since 2003 at the experimental forest of Hokkaido Research Center, FFPRI. We estimated the outcrossing rates of an endemic dwarf bamboo species, Sasa cernua MAKINO, at small-scale flowering sites using six microsatellite loci. We analyzed 1299 seeds, ranging from 23 to 140 seeds from 18 culm at two flowering sites.The multilocus estimate of the outcrossing rates of the dwarf bamboo population was 0.148 (SD 0.118), ranged widely among mother culms from completely selfing, 0.001, to mixed mating, 0.676. The study sites were revealed to be single genet flowerings, however, two culms with the highest outcrossing rates had somatic mutations. The overall inbreeding coefficient of the seeds was high because of predominant selfing although it declined in seedlings, which germinated two years after flowering. This suggests that selection against inbred progenies began early in the establishment process occurring in the natural habitat.