Genetic and ecological evaluation are crucial in effective management of rare and endangered species, including those exhibiting complex breeding systems such as distyly.  We studied a threatened distylous herb Primula reinii in the Hakone volcano, central Japan, to obtain baseline information of reproductive and genetic status towards conservation.  In two representative populations inhabiting a central cone and somma of the volcano, population size, floral morph ratio, stigmatic pollen deposition, and fruit-set were measured.  Using microsatellite markers, we evaluated genetic diversity, structure and differentiation of populations.  Population bottlenecks and historical changes in population size were also estimated from genotype data.  We found significant deviation from equal morph ratios in the central cone population, which also exhibited skewed mating success together with a high frequency of pollination within the same morph.  These trends were not detected in the somma population.  From genetic insights, the central cone population showed slightly lower genetic diversity, whereas no significant deviation from Hardy-Weinberg equilibrium was found in either population.  The estimated moderate genetic differentiation and admixed genetic structure suggest recent lineage divergence and/or gene flow between populations.  While robust evidence for a recent bottleneck was not obtained in our analyses, a clear signature of historical population contraction was detected in the central cone population. Our findings suggest that the skewed morph ratio strongly influenced the reproduction of small and isolated populations in the short-term, highlighting the vulnerability of distylous plant populations under ongoing anthropogenic pressure.