In October to December of 2015, severe outbreaks of a previously unidentified pathogen causing stem rot were observed on celery (Apium graveolens) plants grown commercially in Beijing, China. The initial symptoms manifested as the emergence of a light yellow stripe on the stem. The stripe gradually turns brown and the stem starts to shrink. The last stage of the disease entails rot, accompanied by a fetid odor. When grown on King’s B medium (KB) at 28 °C, colonies of a bacterium isolated from the symptomatic stem were milky white, translucent, and produced fluorescent pigment under ultraviolet light. The 16S rDNA was sequenced (GenBank accession No. MG765472) and showed 99% similarity to that of Pseudomonas marginalis ICMP 3553T (GCA_001645105.1). The characteristic average nucleotide identity was identified based on whole genome sequencing of the bacterium (PKKS00000000), which proved 98% similarity to that of P. marginalis ICMP 3553T (GCA_001645105.1). The traditional physiological and biochemical tests and the Biolog GN2 microplate system (Biolog, Haywood, CA, USA) further confirmed our finding that the culprit pathogen is P. marginalis (Lelliott et al., 1966). Celery plants were inoculated by injecting a bacterial suspension (3 ml/ inoculation plant, 2 × 108 CFU/ml) into the stems, using a sterilized hypodermic needle and were then kept in a moist chamber for 15 days at 28 °C with a 12-h photoperiod. Sterile distilled water was used for inoculating the stems of control plants. Stems inoculated with the pathogen manifested symptoms within 7–10 days similar to those observed in the field. The P. marginalis strains were re-isolated successfully from symptomatic celery to complete Koch’s postulates. No symptoms were present in the controls. Celery bacterial rot caused by P. marginalis (Sumino and Shirai, 2009) has previously been reported in Japan, but to the best of our knowledge, this is the first report of P. marginalis infecting celery in China.