Whitebacked planthopper (WBPH) -resistance in a japonica / indica doubled haploid (DH) rice population established from a cross between WBPH-resistant japonica Chunjiang 06 and susceptible indica TN1, was comparatively evaluated through a field experiment based on the WBPH immigrant density and standardized seedbox screening test (SSST). All the susceptible DH lines in the field experiment behaved accordingly in SSST. However, 35 of resistant 66 lines (53%) in the field, were categorized to susceptible groups in SSST. Likewise, there were no significant differences in WBPH immigrant densities among 70 DH lines that were highly resistant to susceptible in SSST. The results revealed that SSST could not evaluate properly WBPH resistance in the DH lines. Four QTLs for WBPH-resistance phenotyped by the immigrant density were detected on chromosomes 2, 3, 4, and 11. Of them, the QTL on chromosome 4 was the most effective (LOD 21.8, variance 78%). Five QTLs associated with seedling mortality were mapped on chromosomes 2, 3, 4, 5 and 6. In addition to the QTL (LOD 10.5, variance 68%) on chromosome 4, there was another major QTL (LOD 12.7, variance 71%) located on chromosome 5, which was SSST-specific but might be irrespective of the WBPH resistance traits.