Effects of anoxic submergence (1, 5, and 20 h at 5 C) and subsequent aerobic recovery (1, 5, and 24 h at 5 C) on gene expression in organs of the anoxia-tolerant turtle Trachemys scripta elegans were examined. Differential screening of a cDNA library from brains of 20 h anoxia-exposed turtles selected two clones from Anoxic Turtle Brains, ATB1.22 and ATB2.4, as potentially up-regulated by anoxia. The insert of clone ATB1.22 had a single open reading frame that encoded a protein of 376 amino acids which was identified as mitochondrial cytochrome b (CYTb); the sequence was 99% complete and showed 72% of nucleotide residues and 76% of amino acid residues identical to those in the human sequences. Clone ATB2.4 contained an open reading frame encoding 322 amino acids with 65% nucleotide and 63% amino acid sequence identity with another mitochondrial protein, NADH-μbiquimone oxidoreductase subunit 4 (ND4). Northern blot analysis of the time course of gene expression in five organs during 20 h anoxia exposure and 5 h aerobic recovery revealed that Cytb transcript levels increased strongly in livers (5.8-fold within 1 h, remaining high over 20 h) and also in kidneys (rising to threefold higher than controls after 20 h). Nad4 transcript levels also rose strongly in livers (13-fold within 1 h anoxia) and remained approximately fivefold higher than controls over the remainder of the time course. Conversely, Nad4 transcripts in kidneys were unaffected by anoxia but strongly suppressed during aerobic recovery to only 10% of control values after 5 h recovery; transcripts were also reduced in skeletal muscle during recovery. The results suggest that up-regulation of selected mitochondrially encoded genes may be of functional significance to anoxia endurance in these facultative anaerobes.