Although many scientists have primarily concentrated on vegetation restoration in the dry valley of Minjiang River, few species have been demonstrated to be suitable for the restoration now. We investigated seedling emergence, survival, and growth of five endemic species, Bauhinia faberi var. microphylla, Sophora davidii (Franch.) Skeels, Indigofera lenticallata Craib, Oryzopsis munroi Stapf and Miscamthus szechuanesis Keng in order to assess the species′ ability of drought tolerance and the spatial difference in seedling establishment. Seeds of the five species were collected in October 2005 from the dry valleys in Maoxian County, Sichuan Province, China. The seeds were treated with 2.5% of sodium hypochlorite (NaOCl) for 1h and healthy seeds were sowed from May 19 to 23, 2006, for a field experiment. The experiment was arranged using a Completely Randomized Block Design with four factors: two contrasting field sites (wet Zuojishan and dry Lianghekou sites), five species, two microhabitats (vegetated and bareland patches), and three seeding treatments (direct seeding, potted seeding with humus, and potted seeding with soil in dry valley). Seedling survival, height and leaf number were recorded three times: June 25, July 23 and August 23, 2006. All observed species exhibited the flash of seedling emergence after 1 month since sowing. B. faberi var. microphylla, O. munroi and I. lenticallata presented greater seedling emergence and survival than M. szechuanesis and S. davidii. However, dieback of all the seedlings was observed in both study sites after 2 months since seeding, although seedling lived longer in the wet site than in the dry site. The seedling emergence, survival and leaf number of the five species were not significantly affected by microhabitat type and seeding treatments. Nevertheless, seedlings of the five species were more likely to establish under the potted seeding conditions than the direct seeding treatment. These results show that low seedling establishment resulting from environmental stress is a vital factor limiting population regeneration of those native species and vegetation restoration success in the dry valleys of Minjiang River.