Dinoflagellates are a group of eukaryotic microalgae that have many unusual cytological and genomic characteristics. Here, we report the detection of a novel catalase–peroxidase (KatG) gene from the dinoflagellate Prorocentrum minimum, and its transcript levels under copper sulfate (CuSO4) treatment. cDNA analysis yielded a 1,293 bp complete open reading frame (ORF) encoding a 431-amino acid (aa) polypeptide (46.6 kDa). The conserved dinoflagellate splice leader (DinoSL) indicates that this gene is nucleus encoded, and a signal sequence at the N-terminus of the deduced protein indicates that the KatG protein may pass across the endoplasmic reticulum or cytoplasmic membrane, but its precise subcellular location is not known. Unlike the typical KatG proteins, P. minimum KatG (PmKatG) only has one conserved domain (N-domain). Gene expression of PmKatG dramatically increased with increasing concentrations of CuSO4, suggesting that it functions in the defense mechanisms associated with oxidative stress.