Climate conditions such as temperature and light intensity would change steeply along the altitude. Common garden experiments using materials derived from different altitude sources have revealed that altitudinal gradient often generated substantial genetic differentiation between high-altitude and low-altitude population in boreal and temperate conifers. Phenology, growth, physiological traits are often different between high-altitude and low-altitude populations. However, genetic basis of divergent adaptation is poorly understood due to huge genome of conifers. In this study, segregating populations of Abies sachalinensis (2n=24) were made to construct a linkage map and quantitative trait loci (QTLs) of adaptive traits underlying altitudinal divergence were explored. As a mapping population, 239 seedlings from a four-way cross between high-altitude and low-altitude genotypes were used in this study. QTL mapping of phenology, growth, and physiology traits were performed by using the pseudo-testcross strategy based on newly constructed linkage maps with 1,257 markers. The four-way cross strategy with high-altitude and low-altitude populations and numerous SNP markers enabled us to conduct QTL mapping of adaptive traits underlying altitudinal adaptation in non-model organisms with huge genome such as A. sachalinensis.