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Little is known about the difference between bacterial and fungal genetic and functional diversity in karst regions of south China. In this study, the genetic and functional diversity of bacteria and fungi in nine types of soil microenvironments in the karst region in Maolan National Nature Reserve in Guizhou were investigated by PCR-DGGE (Denaturing Gradient Gel Electrophoresis) and BIOLOG EcoPlates. Maolan National Nature Reserve is a UNESCO Biosphere Reserve and plays an important role in protecting the karst forest ecosystem and rare and endangered wild animals and plants in central Asia. The results showed that the diversity of both bacteria and fungi was high and the main factors influencing the diversity of bacteria and fungi were different. The bacterial community structure from different microhabitats under the same vegetation type had higher similarity than similar microhabitats in different vegetation types, which could indicate that the bacterial community structure was mainly controlled by vegetation. For fungi, similar microhabitat species under different vegetation types had higher similarities than different microhabitats species under the same vegetation type, which could indicate that the fungal community structure is mainly controlled by microhabitats. In addition, the metabolic patterns of similar microhabitats in different vegetation were different, while the metabolic patterns of different microhabitats in the same vegetation were not obviously different. In conclusion, the effect of vegetation types on soil microbial functional diversity was greater than that of microhabitats, and this difference was reflected by the different degrees of influence on soil microbial genetic diversity and community structure. [ABSTRACT FROM AUTHOR]