We present a method to find motifs by simultaneously using the overrepresentation property and the evolutionary conservation property of motifs. This method is applicable to divergent species where alignment is unreliable, which overcomes a major limitation of the current methods. The method has been applied to search regulatory motifs in four yeast species based on ChIP-chip data in Saccharomyces cerevisiae and obtained 20% higher accuracy than the best current methods. We also discovered cis-regulatory elements that govern the tight regulation of ribosomal protein genes in two distantly related insects by using this method. These results demonstrate that our method will be useful for the extraction of regulatory signals in multiple genomes.