The PLFAs biomarkers were introduced into analyzing the The diversity of PLFAs biomarkers for the microbial community in the stroma cushion of non-pollution pigsty. The microbial strains of LUODON and LPF #1 were used to treat the stroma cushion in the non-pollution pigsty. The results showed that the efficiency of fomentation on the pig effluent by the two strains were similar. 37 of PLFAs biomarkers were detected out by the MIDI microbial identify system, which constructed the finger printing of the microbial community in the stroma cushion in the non-pollution pigsty. The four most high of PLFAs were the bacteriun biomarker of 16:00 with 431260，bacterium biomarker of 18:1 ω9c with 413075，the anaerobic bacterium biomarker of 18:1 ω7c with 101368，the aerobic bacterium of i15:0 with 90328. The different PLFAs biomarkers were distributed in the different layers of stroma cushion with different densities. The new characteristic index (B) of the PLFAs biomarkers was built up as B=\[PLFAs bacterium PLFAs fungus\]/\[PLFAs actinomycetes PLFAs protest\] to analyze the structure of microbial community. The new fermentation index (F) of the PLFAs biomarkers was built up as F= \[aerobic bacterium PLFAs/anaerobic bacterium PLFAs\] to distinguish the fermentation state in the stroma cushion of pigsty.