The recently reported F420H2-dependent reductases (FDRs) catalyse the reduction of aflatoxins and coumarin via hydrogenation of the α,β-unsaturated moiety. We report that three FDRs (MSMEG_2027, MSMEG_6848 and MSMEG_3356) from Mycobacterium smegmatis also exhibit a different catalytic function towards some aflatoxins through the use of a different cofactor. When F420 was replaced by FMN in these three enzymes, the aflatoxins AFG1 and AFG2 were oxidised via dehydrogenation, producing the reduced cofactor (FMNH2) and an unstable aflatoxin derivative that hydrolyses to an enol with three distinct structural isomers. Both the oxidation and reduction reactions are discussed in detail. This is the first example of an enzyme showing promiscuity for its cofactor leading to divergence of function against the same substrate.