Abstract The devastating citrus disease Huanglongbing (HLB), associated with bacterial pathogens of the genus Candidatus Liberibacter, has spread across many citrus production areas worldwide causing devastating economic losses. In Florida, infection rates in most commercial citrus orchards approach 100 percent by the time trees are 3–4 years old. Most scion cultivars are highly susceptible to Ca. Liberibacter asiaticus (CLas), the pathogen prevalent in Florida, but significant tolerance has been identified within the species Poncirus trifoliata (trifoliate orange) and some of its hybrids that are commonly used as rootstocks. In this study we investigated the relative influence of rootstock and scion in citrus plants composed of susceptible and tolerant cultivars in both the scion and the rootstock position on HLB disease progression and expression of stress and disease-related genes. Experiments were conducted in the greenhouse using the susceptible cultivars ‘Valencia’ orange (Citrus sinensis) and ‘Cleopatra’ mandarin (C. reticulata), and the tolerant trifoliate hybrid cultivars ‘US-802’ (C. grandis × P. trifoliata), ‘US-897’ (C. reticulata × P. trifoliata), and ‘US-942’ (C. reticulata × P. trifoliata). Plants were either mock-inoculated or graft-inoculated with CLas. The incidence of CLas infection at 6 and 12 months after inoculation and the severity of the disease was different among scion/rootstock combinations. Typically, trees with a tolerant cultivar in the scion position contained a lower number of bacteria and were less damaged by infection than trees with a susceptible cultivar in the scion position, regardless of rootstock. Previous observations of significant influence from rootstock on field tree tolerance to CLas may be partially the result of differential rootstock ability to tolerate other stresses, or respond favourably to therapeutic treatments, under the weakened condition caused by the infection. Differential expression of defense-related and other genes found largest fold-differences between non-infected and infected plants when a susceptible cultivar was in the scion position. Fewer genes responded in roots than in leaves, and genes associated with starch metabolism responded strongly and in an opposite direction when comparing roots and leaves, probably indicative of carbon depletion occurring in roots of infected plants.