<p>Pollination success and seed production of clonal plants will depend on the clonal structure of local populations if it affects the degree of geitonogamous pollination. We compared the clonal structure and reproductive performance of an alpine dwarf shrub, <i>Rhododendron aureum</i>, between local populations with different snowmelt conditions in the Taisetsu Mountains of northern Japan. This species is an outcrosser and many self-fertilised ovules are aborted before maturation. Flowering at early snowmelt sites (fellfield and shrubby habitats) occurs in mid-June, when overwintered bumble-bee queens are the major pollinators, whereas flowering at late snowmelt sites (snowbed habitat) occurs after mid-July, when bumble-bee workers are the main pollinators. Fruit-set rates were larger in the early-flowering populations than in the late-flowering populations due to larger queen abundance than usual years. However, seed production in ripe fruits differed between the habitat types in the early-flowering populations, where fellfield population with continuous patch distribution showed higher seed production than shrubby population with fragmented patch distribution. It was supposed that frequent geitonogamous pollination in the fragmented population resulted in higher abortion of self-fertilised seeds. Flower number per inflorescence was similar between flowering times, but ovule number per flower was significantly higher in the early-flowering populations than in the late-flowering populations. The production of many ovules was expected to be advantageous for the early-flowering population to ensure the seed production in environments with fewer flower visitors in usual years. In conclusion, heterogeneous ecological situations in the alpine ecosystem lead to habitat-specific seed production pattern among conspecific populations.</p>