Thanks to its excellent enantiospecificity and efficiency, biocatalysis has become a prominent part of the chemical industry in recent decades. Ene-reductases catalyze the asymmetric reduction of α,β-unsaturated compounds and can be used for the synthesis of valuable enantiopure products. The ‘old yellow enzyme’ (OYE) family of flavoproteins has been the most widely studied and industrially used ene-reductases. Unlike OYE using universal flavin cofactors, F420H2-Dependent Oxidoreductases (FDORs) use unusual deazaflavin cofactor F420, found only in restricted organisms and not yet extensively studied. Considering the similar reactivity profile of OYEs and FDORs, FDORs may also be a potential candidate as a useful ene-reductase, while F420's unique properties may result in better activities, different substrates or compensatory enantiospecificity. Here we showed 2 FDORs, MEMEG_2027 and _2850, can catalyze the reduction of various α,β-unsaturated compounds with good conversion rate and enantopspecificity. It is interesting to note that FDORs tend to show different enantioselectivity from OYEs as well as different preference for substrates, indicating that FDORs may play an important role in complementing the ene-reductases currently used.