Foodborne　bacteria　threaten　human＇s　health.　Capillary　electrophoresis　(CE)　is　a　powerful　separation　means　for　the　determination　of　bacteria.　Direct　separation　of　bacteria　suffers　from　the　shortages　of　low　resolution,　channel　adsorption,　and　bacterial　aggregation.　In　this　work,　a　method　of　nucleic　acid　strand　displacement　was　developed　to　indirect　separate　the　bacteria　by　CE.　DNA　complexes,　consisting　of　probes　and　aptamers,　were　mixed　with　the　three　bacteria　Staphylococcus　aureus,　Escherichia　coli,　and　Pseudomonas　aeruginosa.　The　aptamers　could　specifically　bond　with　bacteria　and　release　the　probes.　Through　the　separation　of　the　probes,　the　bacteria　could　be　indirectly　determined　by　CE.　This　method　avoided　the　shortages　of　direct　separation　of　bacteria.　Under　the　optimized　conditions,　the　three　probes　for　the　bacteria　could　be　separated　and　detected　within　2.5 min　by　high-speed　CE　with　laser-induced　fluorescence　detection.　The　limits　of　detection　for　the　bacteria　were　in　the　range　4.20 × 106　to　1.75 × 107 CFU/mL.　Finally,　the　developed　method　was　applied　on　the　study　of　antagonism　of　the　coexistent　bacteria　to　reveal　the　relationship　between　them.　Furthermore,　the　efficiency　of　bacteriostasis　of　three　traditional　Chinese　medicines,　Coptis　chinensis,　Schisandra　chinensis,　and　honeysuckle,　was　also　studied　by　this　method.　©　2023　Wiley-VCH　GmbH.