We used five simple sequence repeats (SSR) markers to investigate genetic diversity and reproductive system in small populations of Rhododendron brachycarpum disjunctly distributed in the University of Tokyo Hokkaido Forest in Furano, Hokkaido. Levels of genetic diversity were lower for the Furano populations than for the large population in Mt. Hakkoda used in the previous study. Overall FST among all the populations was 0.293 and the populations are significantly differentiated. We found that several individuals with identical genotypes were closely distributed. This finding suggests that this species can be recruited by layering. When we surveyed flowering of the Furano populations in July 2009, only two individuals flowered in the 91 compartment population. As the result of the paternity analysis based on fractional paternity assignment for germinated seedlings derived from the two individuals, we estimated approximately 80% of all the seedlings were generated by self-fertilization.