Objective To identify the most common fungal pathogens and their antifungal drug resistance in autoimmune disease (AD) patients with fungal infection , for guiding the rational use of antifungal therapy. Methods The identification were analyzed by ATB Expression automatic microbiology analytical instrument system. The antifungal susceptibility test was done by ATB FUNGUS strip. Results Of 428 patients studied,36(8.4%) had fungal infections. The most commonly infective sites were lower respiratory tract(53.5%),urinary tract(20.9%), intestinal tract(11.6%). A total of 43 fungi strains were isolated, the most common fungi were Candida albicans (65.1%), Candida glabrata (11.6%), Candida tropicalis (7.0%),and Candida parapsilosis (4.7%).Resistance rates of Candida albicans against ketoconazole, miconazole and econazole were 35. 7% , 46.4% and 32.1% , while resistance rates to fluconazole, amphotericin B, nystain and flucytosine were much lower, being 0, 14.3% , 14.3% and 7.1% . The resistance rates of other fungi were similar to Candida albicans. Conclusion The main pathogens causing fungal infection in patients with AD is Candida albicans. It should as early as possible process the clinical antifungal therapy under the result of antifungal susceptibility test and supportive measure.