The use of proper management strategies for citrus huanglongbing (
HLB
), caused by ‘
Candidatus
Liberibacter asiaticus’ (Las) and transmitted by Asian citrus psyllid (
ACP
) (
Diaphorina citri
), is a priority issue.
HLB
control is based on healthy seedlings, tolerant rootstock cultivars and reduction of
ACP
populations. Here, dynamic populations of Las in different citrus hosts and each instar of
ACP
were studied, together with the seasonal growth and distribution of Las in different tissues, using conventional and TaqMan real‐time
PCR
. Different levels of susceptibility/tolerance to
HLB
were seen, resulting in different degrees of symptom severity and growth effects on hosts or rootstocks. Troyer citrange, Swingle citrumelo and wood apple were highly tolerant among 11 rootstock cultivars. Regarding distribution and seasonal analysis of Las, mature and old leaves contained high concentrations in cool temperatures in autumn and spring. Las was detected earlier through psyllid transmission than through graft inoculation, and the amounts of Las (
AOL
) varied in different hosts. Thus, different
AOL
(10
4
–10
7
copy numbers μL
−1
) and Las‐carrying percentages (
LCP
; 40–53.3%) were observed in each citrus cultivar and on psyllids, respectively. Furthermore, both
AOL
and
LCP
were lower in nymphs than in adult psyllids, whereas the
LCP
of psyllids were not affected by increasing the acquisition‐access time. The present study has significant implications for disease ecology. The combination of early detection, use of suitable rootstocks and constraint of psyllid populations could achieve better management of
HLB
disease.