Gln3p is a GATA-type transcription activator of nitrogen catabolite repressible (NCR) genes. Gln3p was recently found to be hyperphosphorylated in a TOR-dependent manner and resides in the cytoplasm in high quality nitrogen. In contrast, during nitrogen starvation or rapamycin treatment, Gln3p becomes rapidly dephosphorylated and accumulates in the nucleus, thereby activating nitrogen catabolite repression genes. However, a detailed mechanistic understanding is lacking for the regulation of Gln3p nucleocytoplasmic distribution. In this study, we applied a functional genomics approach to identify the nuclear transport factors for Gln3p. We found that yeast karyopherin alpha/Srp1p and Crm1p are required for the nuclear import and export of Gln3p, respectively. Similarly, the Ran GTPase pathway is also involved in the nuclear translocation of Gln3p. Finally, we show that Srp1p preferentially interacts with the hypophosphorylated versus the hyperphosphorylated Gln3p. These findings define a possible mechanism for regulated nucleocytoplasmic transport of Gln3p by phosphorylation in vivo.