The fermentation process of Yunnan arabica coffee is a typical wet fermentation. Its excellent quality is closely related to microbes in the process of fermentation. The purpose of this study was to isolate and identify the microorganisms in the wet method of coffee processing in Yunnan Province, China. Microbial community structure and dominant bacterial species were evaluated by traditional cultivated separation method and PCR-DGGE technology, and were further analyzed in combination with the changes of organic acid content, activity of pectinase, and physical parameters (pH and temperature). A large number of microorganisms which can produce pectinase were found. Among them, Enterobacter cowanii, Pantoea agglomerans, Enterobacteriaceae bacterium, and Rahnella aquatilis were the predominant gram-negative bacteria, Bacillus cereus was the predominant gram-positive bacterium, Pichia kluyveri, Hanseniaspora uvarum, and Pichia fermentans were the predominant yeasts, and all those are pectinase-producing microorganisms. As for the contents of organic acids, oxalic was the highest, followed by acetic and lactic acids. Butyrate and propionate, which were unfavorable during the fermentation period, were barely discovered.