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The article presents the results of studying the enzymatic activity of malate dehydrogenase in amaranth varieties and breeding populations of different ripeness groups and vegetation lengths. The studied amaranth species were A. caudatus L., A. mantegazzianus Passer., A. hybridus L., and A. hypochondriacus L. It was found that the enzymatic activity of malate dehydrogenase ensured the glyoxylate cycle functioning. The malate dehydrogenase activity varied depending on the enzyme accumulation during the initial stages of amaranth plant development. Isoenzyme analysis revealed two isoforms of malate dehydrogenase. It was noted that, in the studied amaranth species, the F-band was intrinsic to the early ripening forms, while the late-ripening carried the S-band. In addition, we detected the malate dehydrogenase polymorphism and differences in the enzymatic activity and demonstrated that it was possible to use them as a biochemical marker in breeding.