Objectives:　To　eveluate　the　potential　application　of　HPLC(High　Performance　Liquid　Chromatography)　to　the　seperation　and　analysis　of　microbe　in　micro-　ecosystem,　so　that　improves　the　sensitivity　and　accuracy　of　the　techniques　of　modern　molecular　biology.　Methods:　Red　kojic　rice　was　selected　as　a　model　system,　bacteria　inside　was　separated　and　recovered　by　the　optimized　sample　preparation　procedure　and　chromatographic　conditions　of　HPLC,　then　analyzed　by　PCR-DGGE　(Denaturing　Gradient　Gel　Electrophoresis)　and　identificated　by　16S　rDNA　sequencing.　Results:　5　fractions　were　recovered,　and　there　were　3　fractions　might　be　pure　strains　based　on　their　electrophoretogram　of　PCR-DGGE.　Direct　sequencing　of　16S　rDNA　of　these　3　fractions　contained　Bacillus　circulans,　Bacillus　ginsengihumi,　Pseudomonas　sp.　or　Alicyclobacillus　respectively.　Conclusions:　This　study　highlights　the　HPLC　technique　could　be　a　rapid,　accurate　and　recoverable　method　for　the　separation　of　pure　strain　from　Red　Kojic　Rice.　Compared　with　the　traditional　PCR-DGGE　technique,　it　can　realize　the　direct　sequencing　of　longer　sequence　of　16S　rDNA　without　gel　recovery.　The　potential　application　of　the　approach　of　chromatographic　separation　in　the　next　generation　sequencing　is　also　discussed.　©　2019,　Editorial　Office　of　Journal　of　CIFST.　All　right　reserved.