We analyzed intron 9 of the OsGI gene in Oryza rufipogon and Oryza sativa in order to investigate evolutionary relationships in rice and the relationship between intron variation and phenotype. OsGI-9 was cloned in 38 O. rufipogon populations and in 139 O. sativa cultivars and the phylogeny was reconstructed. Seed cold tolerance and dormancy were quantified in O. sativa. Three OsGI-9 band types occurred in O. rufipogon: S-type (1.2 kb), F-type (0.9 kb), and FS-type (1.2 and 0.9 kb), whereas only the S-type and F-type occurred in O. sativa. The S-type contains two 255-bp repeats, the F-type contains one 255-bp repeat, and the FS-type contains both. All individuals could be divided into 5 groups in the organism's phylogenetic network: S-type O. rufipogon, F-type O. rufipogon, FS-type O. rufipogon, S-type O. sativa, and F-type O. sativa. F-type O. sativa are most closely related to F-type O. rufipogon and S-type O. sativa are most closely related to S-type O. rufipogon. Statistical analysis indicated that OsGI-9 type is significantly correlated with phenotype; most S-type O. sativa have strong seed dormancy and cold tolerance, and most F-type O. sativa have no seed dormancy and poor cold tolerance.