Lactobacillus in yak ghee at different altitudes in Tibet was screened through tolerance index of resistance to acid, hydrogen peroxide, and antioxidant indicators of scavenging capacity of DPPH free radicals, OH free radicals and superoxide anions. The results showed that 61 strains of bacteria were acquired from Tibet yak ghee, and 7 strains of them were well-tolerated to circumstances of low-acid and hydrogen peroxide. Among the 7 strains, C19 (Lactobacillus plantarum) had the highest scavenging capacity of DPPH free radicals and superoxide anions with the rate of 30.84% and 26.91% respectively. E1 (Lactobacillus rhamnosus) had the highest scavenging capacity of OH free radicals with the rate of 57.60%. No correspondence of scavenging capacity of DPPH free radicals, OH free radicals and superoxide anions was found, and altitude was not directly proportional to the antioxidant activity of Lactobacillus. C19 and E1 had potential in the research and development of natural antioxidants starter.