49 samples selected from main varieties (line) of rice from Ningxia are taken as experimental material, the functional marker of which are subject to analysis and gene sequence comparison at Rf1 gene locus and discrepancies in all materials at various loci are subject to cluster analysis to determine pattern and characteristic of Rf1 locus and offer theoretical reference for transbreeding, molecular marker selection, configuration of hybrid combination and utilization of hybrid vigor of sterile line and restore line. The results show that: （1） 11 varieties (lines) are (Rf1a/Rf1a) genetype, accounting for 22% of main rice variety (line) in Ningxia; （2） Rf1b gene locus detection found mutation at basic group of 17 points, among which loci 2459, 2283, 2059, 1694, 2205, 1784 and 2315 have the highest frequency of mutation among each variety (line), while loci 1576, 1881, 1970 (1985) have the lowest frequency of mutation; （3） The mutations are mainly replacement of nucleic acid characterized by numerous loci, including large variation among varieties (lines) and relevant less insertion mutation locus, only a few varieties (lines). There are about 8 mutation loci in each variety (Line) in average; （4）It is observed from cluster analysis that main rice varieties (lines) in Ningxia could be divided into 3 types, with each type corresponding to main varieties (lines) at different periods, difference of varieties (lines) from the first cluster to the third cluster grows and becomes more diverse, but mutation of each variety decreased from 9 to 7 in average.