To investigate the genetic factors underlying constitutive and adaptive morphological traits of roots under different water-supply conditions, a recombinant inbred line (RIL) population derived from a cross between the lowland rice variety IR1552 and the upland rice variety Azucena with 249 molecular markers, was used in cylindrical-pot experiments. Eighteen QTLs were detected for seminal root length (SRL), adventitious root number (ARN), and lateral root length (LRL) and lateral root number (LRN) on the seminal root at a soil depth of from 3 to 6cm under flooding and upland conditions. One identical QTL was detected under both flooding and upland conditions. The relative parameters under the two water-supply conditions were also used for QTL analysis. Five QTLs for upland induced variations in the traits were detected with the positive alleles from Azucena. A comparative analysis was performed for the QTLs detected in this study and those reported from two other populations with Azucena as a parent. Several identical QTLs for root elongation were found across the three populations with positive alleles from Azucena. Candidate genes were screened from ESTs and cDNA-AFLP clones for comparative mapping with the detected QTLs. Two genes for cell expansion, OsEXP2 and endo-1,4-b-D-glucanase EGase, and four cDNA-AFLP clones from root tissues of Azucena, were mapped on the intervals carrying the QTLs for SRL and LRL under upland conditions, respectively.