Selfed seedlings in conifer tend to exhibit lower survival rate and/or lower growth than outcrossed seedlings. Nevertheless, survival and growth of progeny derived from self-fertilization were similar to those of outcrossing in several populations. In Boso hills, the proportion of self-fertilization of Pinus parviflora populations is known to be high. Two（small and relatively large）populations were used in this study. Mating system of these populations was estimated by simple sequence repeat（SSR）markers. Then, we investigated the relationship between mating system and individual size or resistance against pinewood nematode. We found that selfed progeny exhibited poor growth and the lower resistance rather than outcrossed progeny in the relatively large-size population. In contrast, no significant effects of mating system on individual size and the resistance were detected in the small-size population. When seedlings are produced by seeds collected from a natural forest in a small-size population, selfed progeny will not be excluded through the seedling-production process. Therefore, use of seeds from a small-size population may be problematic, in the point of view of conservation in genetic diversity.