The promoters of eukaryotic genes are being increasingly defined through the identification of consensus DNA sequences, by mutational analysis, and by in vitro and in vivo studies of transcription. Whereas the TATA sequence (Goldberg-Hogness box) has been largely conserved among protein encoding genes (transcribed by RNA polymerase II) of eukaryotes, there is some evidence that other structural and functional determinants of mRNA transcription are not conserved between species. I report there an in vivo comparative analysis of the transcription initiation systems of the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharmyces pombe (which can both be transformed by identical plasmids). I have found no instance in which a gene is transcribed in the same fashion in both yeasts. Instead, I have found that the in vivo transcription starting points for many different yeast genes are determined by the cell in which it is transcribed rather than its gene structure alone. The evidence also suggests that the divergence of the transcription initiation system may partly involve the mechanism or structure which determines the distance from the TATA consensus sequence to the site of transcription initiation.