Objective To identify the Uighur medicine with good antifungal activity via determining the in vitro antifungal activities of 122 kinds of Uighur medicines. Methods The 75% ethanol extracts of 122 kinds of Uighur medicines were prepared by ultrasonic extraction, and anti-deep fungal medicines were screened according to the M38-A2 and M27-A3 broth microdilution method approved by the Clinical Laboratory Standards Institute (CLSI). The broth microdilution checkerboard method was used to determine the synergistic effect of Uighur medicine and fluconazole against drug-resistant Candida albicans. Tannin content was determined by phosphomolybdotungstic acid-casein method, and the relationship between antifungal activity of different extractions and contents of tannin was studied. Results and conclusion At a determination concentration of 2 000 μg/mL, 21 kinds of Uighur medicines such as Terminalia chebula Retz. and Terminalia bellerica Roxb. had inhibitory effect on Cryptococcus neoformans, 15 kinds of Uighur medicines such as Terminalia chebula Retz. and Terminalia bellerica Roxb. had inhibitory effect on Candida albicans, and Curcuma longa L. had inhibitory effect on Aspergillus fumigatus. Curcuma longa L. had the widest antifungal spectrum and showed good inhibitory effect on deep and superficial fungus. Nine kinds of Uighur medicines showed synergistic effects with fluconazole against Candida albicans. Antifungal activity parts of Terminalia chebula Retz., Terminalia bellerica Roxb., Bergenia purpurascens Engl., Acacia senegal Willd and Rhus coriaria L. were concentrated in ethyl acetate, and the minimum inhibitory concentration of different solvent extraction was directly proportional to the content of tannin.