In this study, subtractive PCR was used to isolate a gene that is differentially expressed in the different mating-type cells of Alexandrium tamarense. After three rounds of subtractive PCR using cDNAs synthesized from mRNA of different matingtype cells, amplified PCR products were subcloned into a plasmid vector for construction of subtractive libraries. The dependence on mating type for different levels of accumulated mRNA in randomly selected library clones was confirmed by cDNA membrane array, amplified cDNA Southern blot and RNA dot blot analyses using DIG-labelled probes. One gene, AT4-3, showed a strong and mating-type-specific signal. As a result of sequencing of the complete nucleotide sequence of AT4-3, it was predicted that this gene encodes a protein with 131 amino acid residues. BLAST homology searches of nucleotide and deduced amino acid sequences showed no similarity to any known genes or proteins. The predicted amino acid sequence of AT4-3 has a presumptive N-terminal signal peptide for extracellular secretion, an N-linked glycosylation site and eight cysteine residues in half of the C-terminus. Although the function of this gene is unknown, these results provide the first evidence of intracellular variation between cells of different mating types in dinoflagellates.