‘Candidatus Liberibacter solanacearum’ (Lso) is a phloem-limited bacterial plant pathogen infecting solanaceous plants in the Americas and New Zealand and is associated with diseases of apiaceous crops in Europe, Northern Africa, and the Middle East. This pathogen is also related to other Liberibacter species that infect other crops. In the USA, two haplotypes of Lso, LsoA and LsoB, are predominant and responsible for diseases in potato and tomato. Tobacco, Nicotiana tabacum, a model species to study plant defenses, is a host for Lso; therefore, the interaction between Lso and this host plant could be used to study Liberibacter−plant interactions. In this study, we characterized the infection associated with LsoA and LsoB in tobacco. Under laboratory conditions, LsoB caused more severe symptoms than LsoA, and LsoA and LsoB titers were dynamic during the 7 weeks of the experiment. We also measured SA and other metabolites, including oxylipins, at an early point of infection and found that SA was accumulated in plants infected with LsoB but not with LsoA; whereas ABA levels were reduced in LsoA- but not in LsoB-infected plants.