A Giardia lamblia gene, Glfba, was cloned and sequenced. This gene codes for a 324-residue-long putative class II fructose-1, 6-bisphosphate aldolase. The positions of gaps and phylogenetic analysis with maximum likelihood and maximum parsimony methods showed the sequence to be most closely related to the as-yet uncharacterized aldolases of Helicobacter pylori and Aquifex aeolicus and to the group that comprises the Calvin-cycle aldolases of photosynthetic proteobacteria and cyanobacteria. In combination with the known taxonomic and functional distribution of class I and II aldolases, the results indicate that the G. lamblia enzyme is distinct in its evolutionary history from all eukaryotic fructose-1, 6-bisphosphate aldolases studied so far.