Complementary DNA (cDNA) clones encoding a transcription factor S-II were isolated and characterized. The primary structure of S-II was determined by nucleotide sequence analysis of these clones. The predicted primary structure was consistent with the model that we proposed previously from the results of biochemical analyses of S-II. Using these clones as probes, we analyzed the mRNA for S-II. RNA blot analysis demonstrated the presence of four species of mRNA that hybridized with S-II cDNA in Ehrlich ascites tumor cells. This is the first evidence of polymorphism of mRNA encoding a transcription factor of RNA polymerase II. The results of analysis of the genomic structure suggested that the polymorphism of mRNA may be due to alternative splicing, or differences in initiation or termination of transcription.