In this contribution capillary isoelectric focusing and capillary zone electrophoresis were applied for the separation and detection of different plant pathogens including Pseudomonas syringae pv. syringae, P. syringae pv. lachrymans, Pseudomonas savastanoi pv. fraxinus, P. savastanoi pv. olea, Agrobacterium tumefaciens, A vitis, Xanthomonas arboricola pv. juglandis, X. campestris pv. zinniae, and Curtobacterium sp.. The UV detection and sensitive fluorescence detection of the native phytopathogens or those dynamically modified by the nonionogenic fluorescent tenside based on pyrenebutanoate were used. The isoelectric points of the labeled phytopathogens were found comparable with the pI of the native compounds. No influence of the hosts on pIs of the strains of the genus Pseudomonas was observed. The identification of plant pathogens by gas chromatographic analysis of fatty acid methyl esters was compared with results of capillary isoelectric focusing. Capillary electromigration was successfully applied for the separation of microbes directly from plant tissue suspensions.