Treatment with FLU or c-PTIO affected the expression of Fe acquisition and Na+/H+ antiporter genes in SA03-inoculated Chrysanthemum plants. After 10 days of SA03-inoculation, plants were subjected to saline–alkaline stress for 4 weeks with FLU or c-PTIO treatment. These plants were used to examine the transcription of (A) Fe uptake-related (IRT1, FRO2, and AHA2), (B) Fe transport-related (YSL1, YSL2, FRD3, and NAS1), and (C) Na+/H+ antiporter (NHX1, NHX2, and NHX5) genes by qRT-PCR. Data are expressed as the mean values of three replicates (±SE). Different letters indicate significant differences using two-way ANOVA followed by the Duncan’s multiple range test at P < 0.05.