The yeast Ras-like small GTPases Gtr1p and Gtr2p form a heterodimer and interact genetically with Prp20p, a guanine nucleotide exchange factor for the GTPase Gsp1p. Gtr1p and Gtr2p may be involved in nucleocytoplasmic transport and in the nutrient-responsive TOR signaling pathway, but the role of the Gtr1p-Gtr2p heterodimer is not well understood. Characterization of the Gtr1p-Gtr2p complex is indispensable for understanding the functions of both Gtr1p and Gtr2p. We analyzed the association mode between Gtr1p and Gtr2p. The N-terminus nucleotide binding region of Gtr1p associated with Gtr2p, but not with Ego1p, a protein known to interact with Gtr1p. Gtr1p and Gtr2p are necessary for cells to acquire resistance to caffeine, rapamycin, and hydrogen peroxide. Caffeine treatment released Gtr1p from the high molecular weight Gtr1p-Gtr2p complex. Gtr2p mutants S23N and T44N, but not Q66L, rescued the gtr2 disruptant. Our findings indicate that the formation of heterodimers by Gtr1p differs between Gtr2p and Ego1p.