We studied the flocculation behaviours of microbial communities in 21 soil, wastewater and activated sludge samples to clarify the effects of culture medium types on flocculation ability and screening efficiency, and to analyze diverse functions and microbial compositions. The bioflocculants produced by 33% of the microbial communities had flocculating efficiencies higher than 90%. Six out of the eight microbial communities with efficiencies over 94% were screened from the culture medium using dibutyl phthalate (DBP) as the carbon source. BF-BCT, which was derived from the Chinese cabbage soil sample, had the highest flocculating efficiency (99.6%), species diversity and uniformity. Nine highly efficient strains were separated and purified from seven different microbial communities, indicating that flocculating microorganisms are widely distributed in ecosystems. The 16S rRNA gene testing shows that the eight bacterial and the one fungal strains are common soil microorganisms. The flocculating abilities of BB11 (Sphingobacterium multivorum) and SE3 (Galactomyces geotrichum) have never been reported hitherto. Six strains, including the most flocculating-active TB13 and JB17, were screened from the culture medium using DBP as the sole carbon source. In particular, we compared the performance of culture media and analyzed analogous microbial communities with a Biolog automatic micro-analysis system for the first time.