Burkholderia cocovenenans produces a lethal toxin (Bongkrekic acid) that leads to high fatality in food poisoning cases. However, B. cocovenenans was combined in Burkholderia gladioli in 1999. B. gladioli was originally described as a phytopathogenic bacteria that sometimes causes pneumonia in humans and that acts as an opportunistic pathogen. We thought that it was clinically dangerous to describe these two species without considering their pathogenicities. From our data of 16S rRNA sequence analysis, DNA-DNA hybridization, and fatty acid analysis, we could confirm that B. cocovenenans and B. gladioli should be categorized as a single species. However the species really weaved lethal toxin-producing strains with non-lethal strains. To emphasize that B. gladioli contains two different pathogens, we describe a new pathovar, B. gladioli pathovar cocovenenans, for the lethal toxin-producing strains. We provide characteristics that differentiate this lethal toxin-producing pathovar from other phytopathogenic pathovars within B. gladioli, together with an emended description of B. gladioli.