Abstract:A molecular marker linkage map of F2 population consisting of 104 RFLP markers was employed to identify the quantitative trait loci (QTLs), which control the abilities of rice root to uptake NH4-N and NO3-N and the N use efficiency at seedling stage in a hydroponic experiment Two QTLs linked with ability to uptake NH4-N were detected One of them located on chromosome 2 showed additive and partial dominant gene effects and another on chromosome 5 showed additive and dominant gene effects Two QTLs associated with ability to uptake NO3-N were identified One of them located on chromosome 5 and another on chromosome 6 both showed dominant gene effects One QTL located on chromosome 12 was found to underlying N use efficiency, which showed significant additive and dominant gene effects Furthermore, significant difference was found between means of two parental classes at the marker RG91 on chromosome 4 in the ability of root to uptake NH4-N by t test