Five parents and their near-isogenic lines (NILs) were grown in field experiments in Kunming (elevation 1916 m, two kinds of water temperatures at booting stage were 19.5 +/- 0.7 degrees C and 17.8 +/- 1.1 degrees C) and Aziying (elevation 2150 m, water temperature at booting stage was 18.2 +/- 0.22 degrees C), Yunnan, China, in 2004. Seventeen agronomic traits and SSR molecular markers were clustered by Statistica. The results showed that: (1) The morphological traits of NILs of cold tolerance and recurrent parents (Towada) at booting stage were similar, but the traits related cold tolerance, such as spike neck length, full grains, seed setting rate, anther length, anther volume, were different obviously; (2) using 7 markers had polymorphism between Towada and NILs were chosen from 78 SSR markers, the cold tolerance of NILs proved to be different to Towada. This demonstrates that these NILs were promising population for fine mapping and cloning genes for cold tolerance.