Dwarf bamboo species are monocarpic; they flower simultaneously and die at intervals of several decades. The type of flowering in dwarf bamboo species, including the Sasa genera, ranges from sporadic to gregarious. In this study, by using 6 polymorphic microsatellite markers, we investigated the clonal structure of Sasa cernua, one of the major dwarf bamboo species in central Hokkaido, in a sporadic flowering patch. We have been studying the flowering census in this experimental forest since 2004, and the size of the sporadic flowering patch for S. cernua has been found to be ca. 250 to 1000m². In May 2006, flowering was noted on 60% of living culms on a patch of 1600 m². On this study site, 2529 culms were noted in 1267 clumps, and flowering was observed on 1529 culms of 1177 clumps. Moreover, we detected 12 genotypes in all the 1267 clumps investigated. We identified 5 major clones in these genotypes; 7 of the 12 genotypes were assumed to be generated by somatic mutation. All the flowering clumps belonged to the same clone; however, this clone was found to also include non-flowering vegetative clumps. The other 4 clones did not show any flowering. An important finding of this study is that the flowering of S. cernua is not completely controlled only by clonality.