Abstract: Extracting the complete functional information encoded in a genome, including genic, regulatory and structural elements, is a central challenge in biological research. Prediction of non-protein-coding functional regions, such as regulatory elements, is especially difficult because they are usually short (6-15 bp for S.cerevisiae and many other eukaryotic genomes), often degenerate, and can reside on either strand of DNA at variable distances from the genes they control. Since functional sequences tend to be conserved through evolution, they can appear as ‘phylogenetic footprints’ in alignments of genome sequences of different species. Recently, two groups sequenced several Saccharomyces genomes. The main goal of these studies was to identify the regulatory sites in Saccharomyces spp. using multiple whole-genome alignment or and multiple alignments of gene upstream regions. Results were represented as two lists of predicted binding motifs. Our comparison of these lists shows a rather moderate intersection. This prompted us to analyze the conservation rate for known and predicted binding sites in Saccharomyces genomes in more detail.