Crucian carp (Carassius carassius) avoids lactic acidosis during prolonged periods of anoxia by producing ethanol as the main anaerobic end-product. Apparently, this is made possible by adaptations in the pyruvate dehydrogenase complex (PDHc), which seems to leak acetaldehyde. The acetaldehyde can subsequently be converted to ethanol by alcohol dehydrogenase, a conversion that seems to be restricted to skeletal muscle. The PDHc is a multienzyme complex, consisting of three main units (E1, E2 and E3). I have cloned the E1-subunits E1α and E1β and the E2 enzyme in crucian carp and some related cyprinid fishes, and investigated their sequences and mRNA expression in brain, heart, liver and red muscle using real-time RT PCR. For the E1 subunits, multiple paralogs were found, E1α1-3 and E1β1-2. The extensively deviating E1α3 and E1β2 forms were exclusively expressed in red muscle, where they dominated the expression, making up >94% of the overall E1α- and E1β-subunit expression in this tissue. E1α3 was also found in the ethanol producing goldfish (Carassius auratus) but not in other cyprinid fish studied (zebrafish, roach and common carp). By contrast E1α1,2 and E1β1 were expressed at comparable levels in all investigated tissues, including red muscle. For the E2 enzyme, only one paralog was found. This paralog was also expressed at comparable levels in all investigated tissues. The ubiquitous E1α1,2 and E1β1 paralogs are probably responsible for the normal acetyl-CoA synthesis involved in oxidative ATP production. It is suggested that the muscle-specific E1α3 and E1β2 paralogs are involved in ethanol production in crucian carp, by forming E1 enzymes that produce acetaldehyde.