Fructose-6-phosphate aldolase 1 (FSA) from Aeromonas media (AmFSA) is a class I aldolase characterized by the formation of a Schiff-base intermediate between a conserved lysine residue and a carbonyl substrate. FSA has shown high stereoselectivity and broad substrate spectrum. To provide a structural background for engineering as a catalyst for desired reaction product, AmFSA was cloned and expressed. The purified protein was crystallized from the precipitant of 0.1 M sodium acetate (pH 5.0), 1.4 M ammonium sulfate, and 10 mM β-mercaptoethanol. Diffraction data were collected to 2.1 Å resolution. The crystal belonged to the orthorhombic space group C2221 with unit-cell parameters a = 93.80 Å, b = 175.27 Å, c = 150.99 Å, and α = β = γ = 90°. The spatial positions of the five protein molecules in the asymmetric unit were determined by molecular replacement using the sequentially related Escherichia coli FSA structure.