Expression of microRNA399 (miR399) and P responsive genes was analyzed in white lupin under P stress by miRNA microarray and RT-PCR, respectively. Samples of root (proteoid root and lateral root), stem and leaf were harvested from white lupin plants, which were cultured in hydroponic nutrient solution with or without P for 21 days. Results show that P deficiency significantly increased root biomass of white luipn, but affected negatively shoot biomass and Pi content of the plant. The results of miRNA microarray indicated that 10 members of the miR399 family in root, 7 in stem and 3 in leaf, were up-regulated in the plants under P stress, on average by 4.4, 3.8 and 2.5 folds, respectively.LaATPase, LaPT1, LaMATE, LaPEPC3, LaSAPand LaMDH1 were the 6 P responsive genes, of which expression was much higher in the proteoid roots of the plants without P than in the lateral roots of the plants with P. Putative P responsive elements were found binding transcription factors, PHR1 or WRKY, in the promoter regions of LaPHT1 and LaMATE. Based on the findings, regulatory relationship of miR399 and PHR1 with P responsive genes were explored, suggesting that miR399 and P responsive genes play an important role in white lupin adapting to P deficiency.