A Gram-stain negative, aerobic, rod-shaped and non-spore-forming bacterium, CC-Bw-6T was isolated from chopped tomato stems. Analysis of the 16S rRNA gene sequence of the strain CC-Bw-6T showed its affiliation with the genus Lysobacter within the class Gammaproteobacteria. Strain CC-Bw-6T was found to be most closely related to Lysobacter panaciterrae KCTC 12601T (97.0 %) and Lysobacter daecheongensis KCTC 12600T (96.8 %), and showed lower similarity (<96.5 %) to other Lysobacter species. DNA–DNA relatedness between strain CC-Bw-6T and L. panaciterrae KCTC 12601T was 10.8 %, the G+C content of the genomic DNA is 69.9 mol%. Strain CC-Bw-6T was determined to possess C11:0 iso, C11:0 iso 3OH, C14:0 iso, C15:0 anteiso, C15:1 ω5c, C16:1 ω5c, C16:0, C15:0 iso, C16:0 iso, C17:0 iso and C16:0 10-methyl/C17:1 iso ω9c as predominant fatty acids. The major polar lipid profile consists of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified phospholipids. The predominant polyamine is spermidine, and ubiquinone-8 is the predominant respiratory quinone. Analysis of phenotypic, geno- and phylogenetic characteristics revealed a distinct taxonomic position of strain CC-Bw-6T with respect to other Lysobacter species. Based on the phylogenetic, chemotaxonomic and phenotypic data presented here, we propose a novel species with the name Lysobacter lycopersici sp. nov. The type strain is CC-Bw-6T (=BCRC 80612T = JCM 19164T).