Genomic regions which affected tree growth and wood property traits were investigated in the major plantation tree of Japan, Cryptomeria japonica, in three replicated common garden experiments planted in contrasting environments in Kyushu and Honshu, Japan. Phenotypic traits measured were stem diameter at breast height, tree height, wood strength (Young's modulus), heartwood density, sapwood density, heartwood moisture content, and sapwood moisture content. Quantitative trait locus (QTL) analysis identified an average of 53 QTLs across the three environments. There were two QTLs which affected the same traits across all three environments. These stable QTLs were identified as being associated with sapwood density and Young's modulus and explained 3.5-11.3% and 2.1-18.7% of the total genotypic variation, respectively. In contrast, the majority of QTLs detected were unique to only one environment, a finding which is consistent with QTL mapping studies of other forest trees, indicating a substantial contribution of environmental effects on the mapping progenies. Nonetheless, the two stable QTLs identified in this study could be important genomic regions to target for further research aimed at maximizing breeding efficiency and wood quality of C. japonica across wide environmental gradients.