Center rot of onion, caused by Pantoea ananatis, was first described in the USA, in 1997. P. ananatis is seed-borne in onions and it was suggested that it was introduced into the USA on infected seed lots from South Africa. Center rot has not been observed in South Africa and it was essential to determine if P. ananatis is present in local onion seed. Colonies resembling those of P. ananatis were isolated from four South African seed lots on PA 20, a new semi-selective medium. Pathogenicity tests demonstrated that the South African and America strains induced the same symptoms on onion. Phenotypic and genotypic analyses identified the strains from seed as P. ananatis. In 2004/2005, an unreported disease of maize, brown stalk rot, was observed on commercial fields in South Africa. The representative strains induced disease symptoms similar to those observed in the field. The phenotypic and genotyping tests showed that the strains belonged to the genus Pantoea and separated them into two groups. The first group was identified as P. ananatis. The F-AFLP genomic fingerprints generated by the second group of strains, were distinctly different from those generated by known Pantoea species. To resolve the taxonomic position of Pantoea isolated from onion and maize, sixty-seven strains were subjected to a polyphasic study. The methods used included phenotypic characterisation, genomic fingerprinting, 16S rRNA gene sequence analysis and DNA-DNA hybridisation. The results revealed that the strains belong to three different species within the genus Pantoea: P. ananatis, P. vagens and a novel species, Pantoea allii sp. nov.