Northern hemisphere freshwater ecosystems are projected to experience significant warming and shortening of winter duration in this century. This change coupled with depletion of oxygen (hypoxia) will result in a shift toward fish species with higher optimal temperatures for growth and reproduction that can mitigate hypoxic stress. Here, we tested the assumption that reproduction between two distant species, i.e. anoxic-intolerant common carp (Cyprinus carpio) and anoxic-tolerant goldfish (Carassius auratus), results in the expression of genes responsible for ethanol synthesis (alcohol dehydrogenase and pyruvate dehydrogenase subunit E1β2). The expression of this ethanol-producing pyruvate decarboxylase pathway may transform the biochemical characteristics of progeny into anoxic-tolerant hybrids, expanding their suitable environmental range and potentially increasing invasiveness. Concurrently, a genetic strategy for improving fish tolerance to oxygen-depleted environments will be a valuable physiological trait in fish culture. Differential quantification of gene expression by analyzing mRNA revealed that, compared with koi×koi, koi female×goldfish male (F1 hybrid) possessed the pyruvate dehydrogenase subunit E1β2 gene construct, which was expressed at significantly greater levels in red muscle. The potential of this hybrid to both survive in extreme anoxic conditions and grow at elevated water temperatures would likely contribute to their ecological success.