To establish a genotyping method for Pseudomonas cocovenenans subsp. farinofermentans with fluorescent amplification fragment length polymorphism(FAFLP).Methods Four low-frequency-cleavage restriction endonucleases (ApaⅠ, EcoRⅠ, Hind III, PstⅠ) and two high-frequency-cleavage restriction endonucleases(MseI, TaqⅠ)were tested to optimize the combination for FAFLP. Pre-selective and selective PCR reactions were then optimized. The selective PCR products was separated on LI-COR 4300DNA Analyzer and digital imagines were analyzed by BioNumerics software. In addition, the FAFLP method was compared with other two typing methods(VITEK 2and 16s rDNA).[WT5"HZ]Results 19isolates were clustered into 7groups with 80.85% as the minimum similarity and 98.77% the maximum among groups using the combination of ApaⅠ-G/TaqⅠ-G. The isolates were clustered into 10groups with 48.68% as the minimum similarity and 99.67% the maximum among groups using the combination of PstⅠ-T/TaqⅠ-G. The two combinations of FAFLP could descriminate all the strains in the study, but not the other two methods(VITEK 2and 16s rDNA).ConclusionThe two combinations of FAFLP both had a good discrimination and could be applied for tracing Pseudomonas cocovenenans subsp. farinofermentans in the investigation of foodborne diseases.