Improving the water capturing capacity of its large and deep root system is required to stabilize the yield of upland rice in drought-prone areas in the tropics. For the improvement of the root system through breeding and soil management, it is critical to understand the relative importance of genotypic and environmental effect and their interaction on the root development under various soil conditions and agronomic management. This study aimed to quantify and characterize the effect of genotype and environment, soils and N application levels (0 and 90 kg N ha-1) in the variations of the traits related to the size and distribution of the root system at the flowering stage using 11 rice genotypes in upland fields in southern Luzon in the Philippines. The results indicated that, among the root traits, the genotypic factor accounted for the largest portion of variation for the number of nodal roots, specific root weight (SRW), and R/S ratio, whereas the environmental effect was relatively large for deep root length ratio (DRR) and total root dry weight (RDW). Especially, the DRR, the ratio of root length at deeper than 30 cm per unit area to the RDW, was strongly affected by the site. Nitrogen application increased RDW without a substantial change in the R/S ratio and DRR. On the other hand, significant genotypic variations of RDW and DRR were obtained, which may imply the opportunity for the genetic improvement. Japonica upland varieties showed a large RDW (90-111 g m-2) associated with high R/S ratio (0.18-0.23) and a high SRW (0.26-0.27 mg cm-1), whereas aus (Dular) and indica (Vandana) upland varieties had a large DRR (12.5-13.8 m g-1) with a medium R/S ratio (0.14-0.17), suggesting an efficient formation of a deep root system with a limited biomass allocation to the roots. In addition, the analysis of G x E interaction term for RDW by an Additive Main Effects and Multiplicative Interaction (AMMI) model indicated that the response to soil conditions also differed b