Alfalfa is widely grown worldwide for its excellent nutritional value.Pantoeaspecies living in alfalfa seeds can easily spread over great distances with frequent trade. However, the pathogenic properties of this dangerous hitchhiker on alfalfa have not been evaluated. Here, we identified the taxonomic status ofPantoeastrain CQ10 isolated from the interior of alfalfa seeds based on the whole genome sequence. The diverse virulence attributes of strain CQ10 during host infection were characterized through pathogenicity assays and functional and genomic analyses. We report that strain CQ10 belongs to a novel species in the genusPantoea, which was phylogenetically close toPantoea vagansandPantoea agglomerans. Strain CQ10 caused bacterial leaf blight of alfalfa after inoculation from the roots. We found that strain CQ10 possesses a large number of pathogenic genes involved in shaping the virulence properties during bacteria–host interactions, including motility, biofilm, type VI secretion system, and nutrient acquisition. Compared withP. vagansandP. agglomerans, the unique virulence factors of strain CQ10 were mainly involved in motility and biofilm, which were confirmed by in vitro experiments. Taken together, our results suggest that strain CQ10 is the firstPantoeaspecies to infect alfalfa, and it possesses diverse virulence attributes among which motility and biofilm may be the best weapons.