Tomato is the most produced and consumed vegetable in Turkey, and has a great importance in farmers’ income. In this study, bacterial disease surveys were carried out in 130 plastic covered greenhouses in the center and eight district neighborhoods of Mersin province, Turkey from January to May, 2019 and 2020 growing periods, respectively. Suspicious tomato plants showing typical disease symptoms such as stem rot, pith necrosis and secondary root formation on the stem were collected from twelve different greenhouses. The representative bacterial strains (n = 20) were initially characterized based on pathogenicity test on tomato seedlings, phenotypic characteristics, and then identified as Stenotrophomonas spp., and Paenibacillus spp. according to their protein fingerprint patterns obtained by MALDI TOF MS system. The identification of three strains was further confirmed by sequencing of 16 S rDNA. According to BLAST analysis, the strains shared 99–100% identity with Stenotrophomonas rhizophila, Stenotrophomonas chelatiphaga and Paenibacillus amylolyticus strains deposited in GenBank. The prevalences of tomato inner pith necrosis and stem rot caused by Paenibacillus amylolyticus and Paenibacillus polymxa and pith necrosis caused by Stenotrophomonas spp. were 0.8% and 4.6%, respectively in the area. Representative bacterial strains were further tested for copper sensitivity in vitro, and, all strains were resistant for 1 mM copper amended KB media. This study represented the first report of newly introduced stem and core rot and pith necrosis caused by Paenibacillus amylolyticus, Paenibacillus polymxa and Stenotrophomonas spp., on tomato in Turkey.