GmPHR1 from soybean (Glycine max) was isolated and characterized. This novel homolog of the AtPHR1 transcription factor confers tolerance to inorganic phosphate (Pi)-starvation. The gene is 2751 bp long, with an 819-bp open reading frame and five introns. Analysis of transcription activity in yeast revealed that the full-length GmPHR1 and its C-terminal activate the reporter genes for His, Ade and Ura, suggesting that the C-terminal peptide functions as a transcriptional activator. Quantitative real-time PCR indicated that patterns of GmPHR1 expression differed. For example, under low-Pi stress, this gene was quickly induced in the tolerant JD11 after 0.5 h, with expression then decreasing slowly before peaking at 12-24 h. By contrast, induction in the sensitive Niumaohuang (NMH) was slow, peaking at 6 h before decreasing quickly at 9 h. GmPHR1 showed sub-cellular localization in the nuclei of onion epidermal cells and Arabidopsis roots. Growth parameters in wild-type (WT) Arabidopsis plants as well as in overexpression (OE) transgenic lines were examined. Under low-Pi conditions, values for shoot, root and whole-plant dry weights, root to shoot ratios, and lengths of primary roots were significantly greater in OE lines than in the WT. These data demonstrate that GmPHR1 has an important role in conferring tolerance to phosphate starvation.