The dinoflagellates have some primitive nuclear fearures and are evolurionarily intermediate between prokaryotes and eukaryotes. The small subunit ribosomal RNA gene, the large subunit robosomal RNA gene, the 5.8S ribosomal RNA gene and the internal transcribed spacer (ITS) of Gonyaulax polyedra were cloned, and their sequences were analyzed to better understand their evolutionary position. The small unit of ribosomal RNA gene was 1,794 nt long, the large subunit ribosomal gene was approximately 3,500 nt long, and the 5.8S ribosomal RNA gene was 159 nt long. The first internal transcribed spacer (TTSI) was 191 nt long, and the second internal transcribed spacer (ITS2) was 185 nt long. The intergenic spacer of ribosomal RNA gene (IGS) was about 2,200 nt long, indicating that 5,800 nt of transcribed sequences were separated by roughly 2,200 nt of intergenic spacer. The ribosomal RNA genes were repeated many times and arranged in a head-to-tail tandemly repeated manner. The repeating unit of ribosomal RNA gene of G. polyedra was proposed to be 8,000 nt long. Based on the lengths of ribosomal RNA, sequence aligruments with representative organisms, and phylogenetic analysis on ribosomal RNA. G. polyedra appears to one of the alveolates branched from the eukaryotic crown and among dinoflagellates it seems to have emerged not early.