Foodborne　pathogenic　bacteria　always　threaten　human　health.　Flavonoids　are　commonly　used　in　antibacterial　applications.　Studying　the　antibacterial　effect　of　flavonoids　on　bacteria　is　significant.　Capillary　electrophoresis　is　a　versatile　separation　means.　It　has　different　separation　modes,　so,　it　can　be　applied　in　the　analysis　of　both　bacteria　and　flavonoids.　In　this　study,　an　efficient　method　of　indirect　separation　and　detection　of　three　bacteria　Vibrio　parahaemolyticus,　Escherichia　coli,　and　Staphylococcus　aureus　was　developed.　The　determination　of　bacteria　was　realized　by　separating　the　aptamers　corresponding　to　the　bacteria　by　capillary　sieving　electrophoresis.　This　method　avoided　the　disadvantages　of　low　resolution,　channel　adsorption　and　bacterial　aggregation,　encountered　in　the　direct　separation　of　bacteria.　The　separation　of　the　flavonoid　kaempferide　was　realized　by　capillary　zone　electrophoresis,　and　kaempferide　in　Kaempferia　galanga　was　determined.　Kaempferide　and　the　extract　of　Kaempferia　galanga　were　applied　in　the　antibacterial　tests　separately.　Using　the　developed　method,　the　bacterial　growth　curves　and　the　curves　of　the　kaempferide　concentration　were　studied　respectively.　The　results　showed　that　both　kaempferide　and　Kaempferia　galanga　could　effectively　inhibit　the　bacteria.　The　inhibitory　effect　on　the　terrestrial　bacteria　Escherichia　coli,　and　Staphylococcus　aureus　was　better　than　that　on　the　marine　bacterium　Vibrio　parahaemolyticus.