SUMMARYThe mitochondrial (mt) genomes of dinoflagellates are not completely sequenced due to frequent recombination events resulting in a shortage of information about the dinoflagellate mt genome. To obtain a large amount of information, we characterized 14 polymerase chain reaction (PCR) fragments of more than 27 kb of the mt genome of the toxic dinoflagellateAlexandrium catenellaWhedonetKofoid (Balech) using thecobandcox1genes, the only identified functional mt genes ofA. catenellaexcluding rRNA fragments. The mt PCR clones encode multiple copies of cytochromeb(cob) and cytochromecoxidase subunit 1 (cox1) bearing several types of 5′ or 3′ sequences, and two rRNA fragments showing sequence similarity with a large subunit (LSU) rRNA D fragment and LSU RNA2 of apicomplexa. Each mt PCR clone showed different gene arrangements and intergenic sequences suggesting multiple contexts in the mt genome ofA. catenellaand frequent homologous recombinations. Reverse transcription PCR analysis suggested some types of the multiple copies ofcobandcox1genes are likely non‐transcriptional. Further,A. catenellamt mRNAs lacked in‐frame termination codons and a canonical initiation codon, excluding an ‘atg’ codon incobmRNA. However, we successfully detected the activity of the electron transport proteins suggesting mt translation requires no canonical initiation and termination codons.