The citrus industry in Florida faces a destructive endemic disease, known as huanglongbing (HLB), associated with Candidatus Liberibacter asiaticus (CLas), a phloem-limited bacterium, and transmitted by the Asian citrus psyllid (ACP). Rootstocks are regarded as critical to keep citrus production commercially viable and help trees cope with the disease. Although most scions are susceptible, some rootstocks are HLB-tolerant and may influence ACP infestation and CLas colonization and therefore the grafted tree tolerance. This study aimed to elucidate the relative influence of rootstock and scion on insect vector infestation and CLas colonization under natural HLB-endemic conditions. Seven commercial rootstock cultivars with different genetic backgrounds were grafted with ‘Valencia’ sweet orange (Citrus sinensis) or were self-grafted (non-‘Valencia’) and planted in an open field where ACP and CLas were abundant. ACP infestation was determined weekly during periods of leaf flushing, and leaves and roots were analyzed every 3 months to determine CLas titers. Trees with ‘Valencia’ scion were more attractive to the psyllids than non-‘Valencia’ scions. This was also associated with a higher number of bacteria and a larger abundance of foliar HLB symptoms. The influence of the rootstock on the psyllid attraction of grafted ‘Valencia’ scion was less evident, and leaf CLas titers were similar regardless of the rootstock. Among the non-‘Valencia’ scions, Carrizo had the lowest and US-942 the highest leaf CLas titers. Root CLas titers also varied among cultivars, and standard sour orange roots harbored more bacteria than some trifoliate orange hybrid rootstocks such as US-942. In some trees, CLas was detected first in the roots 4 months after planting, but root CLas titers remained low throughout the study. In contrast, leaf CLas titers increased over time and were considerably higher than root titers from 7 months until the end of the study, 15 months after planting. Overall, the results of this study demonstrate a greater relative influence of the scion than the rootstock on ACP infestation and CLas colonization during the early stages of infection. This suggests that other cultivar-specific traits, such as the ability to tolerate other stresses and to absorb water and nutrients more efficiently, along with influences on the scion phenology, may play a larger role in the rootstock influence on the grafted tree tolerance during the later stages of HLB progression.