Aldolase exhibits multiple functions in a variety of organisms, including fungi, unicellular algae and plants, and so on. Furthermore, different isoforms of fructose 1,6-bisphosphate aldolase (FBA) exhibit significantly different characteristics and functions. This review describes the structures, characteristics, and functions of FBAs derived from diverse organisms, including FBA II in pathogen microorganisms, as well as FBA I mainly in unicellular algae and plants. Differences between FBA and FBP aldolase-phosphatase bifunctional enzyme (FBA/P) are also discussed. Finally, we suggest several potential research questions regarding the functions of FBA in higher plants.