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Two major gene duplication events are thought to have taken place in the evolution of creatine kinases (CK) in the vertebrates - (1) the formation of distinct mitochondrial (MiCK) and cytoplasmic forms from the primordial gene and (2) subsequent formation of the sarcomeric (sar-) and ubiquitous (ubi-) isoforms of octameric MiCK and muscle (M) and brain (B) isoforms of dimeric, cytoplasmic CK. The genes of these two CK clades reflect a distant divergence as sar- and ubiMiCK genes consistently have nine protein-coding exons while M- and B-CK genes have seven protein-coding exons; these genes share only one common exon. CKs are also widely distributed in the invertebrates and it has recently been shown that MiCKs evolved well before the divergence of the major metazoan groups. In the present communication, we report the structure and topology of the gene for MiCK from the protostome marine worm Chaetopterusvariopedatus. The protein-coding region of the gene for this primitive MiCK spans over 10 kb and consists of eight exons, the last five (E4–E8) have identical boundaries to the corresponding exons of sar- and ubiMiCK genes. Exon-3 of the C.variopedatusMiCK gene consists of the corresponding E3 and E4 of the vertebrate MiCKs with no intervening intron. E1 is longer and E2 is shorter in the polychaete MiCK gene than the counterpart sarcomeric and ubiquitous genes. The insertion of the intron in C.variopedatusE3 creating the two exons as well as the rearrangement of the intron between E1 and E2 must have occurred prior to or coincident with the duplication event creating the two vertebrate mitochondrial isoforms. Sarcomeric and ubiMiCKs display substantial differences from their invertebrate MiCK counterparts in properties relating to octamer stability and membrane binding. The evolutionary changes in gene topology may be a component of this functional progression.