Center rot of onion is caused by the Gram-negative bacterium Pantoea ananatis. The goal of this research was to use multilocus sequence analysis, virulence assays, and phenotypic tests to determine the genetic diversity of 50 P. ananatis strains isolated from various sources in Georgia over the past two decades. After sequencing six housekeeping genes (fusA, gyrB, leuS, pyrG, rplB, and rpoB) and amplifying genomic fingerprints using repetitive extragenic palindromic polymerase chain reaction (Rep-PCR), phylogenetic analyses exhibited little genetic diversity at the core genome. However, we observed extensive phenotypic variation among 33 isolates tested for pathogenicity and aggressiveness on multiple Allium hosts. Moreover, phenotypic diversity did not correlate with genetic phylogeny. After screening strains from our collection that were isolated in Georgia, we identified a new pathogen on onion that had been misidentified as P. ananatis. Characterization of a new center rot causing agent, P. stewartii subsp. indologenes, was conducted using a polyphasic approach. We also investigated the effect growth stage inoculation and cultivar had on bulb incidence before curing and after curing, as well as total incidence. For precured bulbs, inoculating onions at first leaf senescence (62%) exhibited a higher mean incidence than bulbs that were inoculated at bulb initiation (37%) and bulb swelling (31%) stages. Inoculating plants at bulb initiation (29%) and bulb swelling (31%) displayed a higher mean incidence for cured bulbs than first leaf senescence (6%). When total bulb incidence was calculated, first leaf senescence (64%) had a significantly higher mean incidence than bulb initiation (52%) and bulb swelling (55%) stages. Of the cultivars tested, Granex YPRR (84%) recorded the highest bulb incidence, while 1407 (33%) and 1518 (49%) recorded the lowest incidences. Lastly, we tested the efficacy of Actigard, Kocide 3000, and Actigard + Kocide 3000 as protective foliar treatments from center rot bulb infection at bulb initiation and bulb swelling and if thrips feeding impacted efficacy of treatments. Treatments containing Kocide 3000 were most effective at both growth stages, however when thrips were present, treatments were not significantly different than untreated control.