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To study the genetic polymorphism and ecological diversity of clinical Penicillium marneffei strains isolated from local regions in China.50 clinical strains isolated from Guangxi, Guangdong and Guizhou provinces were identified by morphological and molecular methods, and were analyzed by Multilocus Microsatellite Typing (MLMT) method and software SPSS 18.0;the results of MLMT showed that the Penicillium marneffei microsatellite loci, PMMⅠ, PMMⅡ and PMMⅢ loci detected 29, 9 and 8 alleles respectively.