Fructose bisphosphate aldolases (FBAs) catalyze the reversible cleavage of fructose 1,6‐bisphosphate into dihydroxyacetone phosphate and glyceraldehyde 3‐phosphate. We analyzed two previously uncharacterized cytosolic Arabidopsis FBAs, AtFBA4 and AtFBA5. Based on a recent report, we examined the interaction of AtFBA4 with calmodulin (CaM)‐like protein 11 (AtCML11). AtFBA4 did not bind AtCML11; however, we found that CaM bound AtFBA5 in a Ca2+‐dependent manner with high specificity and affinity (KD ~ 190 nm) and enhanced its stability. AtFBA4 and AtFBA5 exhibited Michaelis–Menten kinetics with Km and Vmax values of 180 μm and 4.9 U·mg−1 for AtFBA4, and 6.0 μm and 0.30 U·mg−1 for AtFBA5, respectively. The flavonoid morin inhibited both isozymes. Our study suggests that Ca2+ signaling and flavanols may influence plant glycolysis/gluconeogenesis.