To clarify the factors affecting the seedling establishment of the subalpine stone pine (Pinus pumilaRegl.) from nutcracker‐cached seeds, subsequently emerged seedlings were examined in two plots on Mt Akitakomagadake, northern Japan. The survivorship of older seedlings (2–20 years old) was also monitored during six seasons at nine different sites. In one plot with 18 caches, seed germination occurred between June and mid‐July. During this period, nutcracker’s retrieved the stored pine seeds from 16 caches and ate some seeds immediately. Simultaneously, this nutcracker behavior caused mechanical damage to newly emerging seedlings (e.g. uprooting and tearing off cotyledons). Such initial loss to in situ harvesting and mechanical damage accounted for 75% of the total seeds remaining in the caches. The number of established current seedlings sharply declined during the first 2 years, and the survival rate was 4.4% over four winters. Two major mortality factors were identified: uprooting by frost‐heave soil disturbance in the spring of the second year and standing death by drought or other physiological stresses in early summer. In another plot with 13 caches, survivorship of newly emerged seedlings was also low (4.2%), but mortality was mostly due to summer drought, indicating that the frost‐heave event was a site‐specific disturbance factor. For older seedlings, survival rates reached approximately 90% even after six seasons and summer drought stress was a major mortality factor. My findings suggest that seedling recruitment ofP. pumilawas largely limited by both nutcracker disturbance and external disturbance (and/or stresses) at an early stage. However, after the critical first few years, pine seedlings were highly likely to survive and grow to the sapling stage despite the harsh environment of the high mountains.