Abstract:[Background] Quinoa is an example of functional food that is popular all over the world, while little has been reported about the endophyte Trichoderma afroharzianum of quinoa seeds. [Objective] To determine the antimicrobial activity and growth-promoting effect of endophytic fungi isolated from quinoa seeds. [Methods] The isolated endophytic fungi were identified based on morphology and the ITS, tef1, and rpb2 gene sequences characteristics. The antimicrobial effects of endophytic fungi were determined by plate confrontation method and plate culture method. The growth-promoting effect of the strain on quinoa was determined by pot experiment. [Results] The strain LMNS-M9 was identified as T. afroharzianum. The mycelial growth and sporulation of strain LMNS-M9 were promoted at 30 ℃, pH 5.0, and the presence of magnesium ion. Glucose, lactose, peptone, and potassium dihydrogen phosphate were suitable for mycelial growth of strain LMNS-M9, and glucose, ammonium nitrate, and dipotassium hydrogen phosphate were suitable for sporulation. LMNS-M9 showed inhibitory activity against Botrytis cinerea, Ascochyta caulina, Fusarium citri,Alternaria alternata, and Trichothecium roseum, with the inhibition rates of 12.53%, 51.96%, 52.38%, 59.25%, and 62.04%, respectively. The volatiles showed the inhibition rates of 35.86%, 61.54%, 33.33%, 41.95%, and 59.09%, respectively. LMNS-M9 could contact or entangle the mycelia of pathogens (B. cinerea, A. caulina, F. citri, and A. alternata) to rupture or lyse the mycelia. The pot experiment showed that LMNS-M9 advanced the germination of quinoa seeds by 2 days. Furthermore, LMNS-M9 increased the root length, underground fresh weight, and underground dry weight of quinoa seedlings by 71.88%, 104.66%, and 68.89%, respectively. [Conclusion] The endophytic fungus isolated from quinoa seeds was identified as T. afroharzianum. It inhibited the growth of five pathogens and promoted the root growth of quinoa, demonstrating good biocontrol potential.