Flax is an important natural fiber raw material. The application of pectase enzyme in flax retting, which was produced by microorganism, can improve the fiber quality, shorten the retting period and reduce wastewater emissions, and has broad application prospects. However, different retting methods affect the production cycle and fiber quality.

In order to investigate the bacterial community diversity and dominant bacterium of warm water retting liquid and enzymatic retting liquid, the samples were studied by using DGGE under laboratory conditions.

We found Pseudomonas of Gammaproteobacteria and Uncultured bacteria were the dominant bacterium, accounting for 45.5% and 36.4% respectively, in the sequences of warm water retting liquid samples. Pseudomonas of Gammaproteobacteria was also the dominant bacterium, accounting for 50% in the sequences of enzymatic retting liquid samples. Bacillus of Firmicutes occurred along with the whole process of warm water retting and enzymatic retting liquid samples. However, in addition to share the dominant bacterium, there are also some differences in bacterium between the two liquid samples, such as Lactococcus, Flavobacterium and other bacterium which discovered in enzymatic liquid samples were not found in warm water liquid samples.