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Purpose: To isolate and identify the fungal endophytes of Fagopyrum tataricum and assess their antimicrobial activity. Methods: The fungal isolates were identified according to their morphological characters and internal transcribed spacer (ITS) sequence analysis. Both broth-dilution-colorimetric assay and spore germination test were employed to assess the antimicrobial activity of fungal mycelia extracts. Results: A total of 72 endophytic fungal isolates were successfully obtained from the healthy tissues of F. tataricum. On the basis of their morphological and molecular characteristics, thirteen distinct fungal isolates were identified, and belonged to Alternaria, Bionectria, Botryosphaeria, Fusarium, Guignardia, Nectria, Neonectria, Phomopsis, Pseudocercospora and Verticillium spp. Of these, Pseudocercospora owned the maximum colonization frequency (15.3 %), next for Alternaria (12.5 %) and Neonectria (11.1 %). Through antimicrobial screening assays, six endophytes (Fataf-4, 6, 9, 11, 12 and 15) were active against Bacillus subtilis, Staphylococcus aureus, Agrobacterium tumefaciens, Escherichia coli and Pseudomonas lachrymans, and their minimal inhibitory concentration (MIC) ranged from 0.125 to 2.00 mg/mL. Furthermore, the endophytes, Fataf-9 and Fataf-11, also displayed strong inhibitory activity on the spore germination of F. oxysporum f. sp. vasinfectum and F. oxysporum f. sp. cucumerinum, and their median effective inhibitory concentration (IC50) was 0.356, 0.463, 0.451 and 0.489 mg/mL, respectively. Conclusion: The endophytic fungi of F. tataricum appear to be diverse and promising in their antimicrobial activity, and may represent a potential source of antibiotics for agriculture and/or pharmaceutical applications. [ABSTRACT FROM AUTHOR]