Phosphate is essential for cell metabolism in all organisms. As it is often limiting in the soil, plants have evolved various mechanisms to cope with low-phosphate conditions. Here, we report that Aluminum Sensitive 3 and NAP3, two genes previously identified to function in aluminum tolerance, play a critical role in plant response to phosphate deficiency. Two T-DNA insertional alleles of ALS3 gene in Arabidopsis showed hypersensitive responses to phosphate limiting conditions. Compared to the wild type, als3 mutant plants exhibited more severe root growth inhibition and developed more root hairs under phosphate starvation. Interestingly, these phenotypic changes occurred only when the low-phosphate medium is supplemented with sucrose, suggesting that ALS3 regulates low-phosphate response in a sugar-dependent manner. Furthermore, NAP3, a gene encoding the nucleotide binding domain protein that physically interacts with ALS3, was implicated in the same pathway in response to low-P. The nap3 mutant showed the same phenotype as the als3 mutant when grown on phosphate depletion medium. We conclude that ALS3 and NAP3 protein form an ABC transporter complex that is required for sugar-dependent response to phosphate deficiency.