Abstract: A method for breeding an improved variety of a forage sorghum-Bacillus megaterium symbiont, and a CAPS marker for rapidly identifying Bacillus megaterium BM18-2. The method includes: when a stigma of a female parent is exerted for 2-3 d, spraying a Bacillus megaterium solution to the stigma, then pollinating same with pollens from anthers of a male parent after the anthers are exerted for 2-5 d, and harvesting mature seeds. The CAPS marker mainly includes a primer pair designed for an SNP site and endonuclease BspT104I, and upstream and downstream primers are respectively SEQ ID Nos: 1-2. The first method for breeding improved variety of forage sorghum containing endophytic Bacillus megaterium. Produced seeds can significantly increase biomass, crude protein, soluble sugar content and roughage grading index (GI) of plants grown in soil with a salt content ?8‰; and the CAPS marker can realize rapid qualitative identification of Bacillus megaterium BM18-2.