Modern agriculture and plant breeding must continuously meet the high and increasingly growing requirements of consumers and recipients. In this context, one of the conditions for effective management of any farm is access to quick and efficient diagnostics of plant pathogens, the result of which, together with the assessment of experts, provide breeders with tools to effectively reduce the occurrence of plant diseases. This paper presents information about biodiversity and spectrum of endophytic and phytopathogenic bacterial species identified in plant samples delivered to the Plant Disease Clinic in 2013–2019. During the tests, using the Biolog Gen III system, the species affiliation of the majority of detected bacterial strains found in plant tissues as an endophyte and not causing disease symptoms on plants was determined. These data were compiled and compared with the number of found identifications for a given species and data on the pathogenicity of bacterial species towards plants. In this way, valuable information for the scientific community was obtained about the species composition of the bacterial microbiome of the crop plants studied by us, which were confronted with available literature data. In the study, special attention was paid to tomato, which is the plant most often supplied for testing in the Plant Disease Clinic due to its economic importance.