Subunit VIa of mammalian cytochrome c oxidase (COX; EC 220.127.116.11) exists in two isoforms, one present ubiquitously ('liver' isoform; COX VIa-L) and the other present only in cardiac and skeletal muscle (COX VIa-M). We have now isolated a full-length cDNA specifying human COX VIa-M. The deduced mature COX VIa-M polypeptide is 62% identical to the human COX VIa-L isoform, but is approximately 80% identical to the bovine and rat COX VIa-M isoforms, suggesting that the two COX VIa isoform-encoding genes arose prior to the mammalian radiation. Transcriptional analysis showed a tissue-specific pattern: whereas COXVIa-L is transcribed ubiquitously, COXVIa-M is transcribed only in heart and skeletal muscle. The cDNA specifying COX VIa-M is a prime candidate for use in investigations of Mendelian-inherited COX deficiencies with primary involvement of muscle.