Glutathione S-transferase (GST) is important in plants to resist various stresses. In this study, two Phi GST genes (SmGSTF1 and SmGSTF2) were cloned from Selaginella moellendorffii. SmGSTF1 and SmGSTF2 genes encode proteins of 215 amino acid residues. Gene expression analysis showed that the two genes were expressed in roots, stems and leaves. The recombinant SmGSTF1 and SmGSTF2 proteins were overexpressed in Escherichia coli, and purified by Ni-affinity chromatography. SmGSTF1 and SmGSTF2 had the catalytic activity towards 1-Chloro-2,4-Dieitrobenzene, 4-Chloro-7-nitro-1,2,3-benzoxadiazole (NBD-Cl), and 4-Nitrobenzyl chloride substrates. SmGSTF1 also had the activity towards Fluorodifen and Cumyl hydroperoxide (Cum-OOH), whereas SmGSTF2 not. The enzyme kinetics analysis showed that SmGSTF1 and SmGSTF2 had high affinity towards glutathione, and low affinity towards 1-Chloro-2, 4-Dieitrobenzene. The enzymatic activity of SmGSTF1 and SmGSTF2 had high catalytic activity between pH 7 and 8.5, and between 45 and 55 °C. SmGSTF1 and SmGSTF2 may have an important role in the resistance of Selaginella moellendorfii against stress.