Huanglongbing (
HLB
), caused by ‘
Candidatus
Liberibacter asiaticus’ (Las), is a devastating disease of citrus trees in Florida. Previous work showed that the rootstock cultivar Cleopatra mandarin (
Citrus reticulata
) has a higher population of Las in roots than Swingle citrumelo (
C. paradisi
×
Poncirus trifoliata
). Las reduced fibrous root biomass and sucrose content in Cleopatra mandarin more than in Swingle citrumelo. To understand the mechanisms for susceptibility to Las infection, sucrose and hormone metabolism status were evaluated in Cleopatra mandarin and Swingle citrumelo. In fibrous roots of Cleopatra mandarin, higher expression of genes related to sucrose cleavage was consistent with lower sucrose content compared to noninoculated seedlings at 5 weeks post‐root trimming (wpt). In fibrous roots of Swingle citrumelo, both sucrose content and gene expression related to sucrose cleavage were less disrupted by Las infection compared to Cleopatra mandarin at 5 wpt. Genes associated with salicylic acid (
SA
), ethylene (
ET
) and abscisic acid (
ABA
) synthesis, and
ABA
signalling, phospholipases D (
PLD
), and phospholipase A2 (
PLA
2) were activated by Las infection at 5 wpt in Cleopatra mandarin. Expression of downstream effectors of
SA
, i.e.
NPR
1,
WRKY
70 and
PR
1, did not change in Cleopatra mandarin, suggesting inhibition of the response to
SA
by the elevation of
ABA
,
ET
and
PLD
. In contrast, the up‐regulation of
PR
1, lower response of sucrose metabolism genes and down‐regulation of biosynthesis of phytohormones indicates that Swingle citrumelo activates a more effective defence against this biotrophic pathogen than Cleopatra mandarin.