The genetic maps of bacteriophages Mu and lambda can be aligned with respect to the functions of their genes. We were interested to ascertain whether the congruence of gene order is reflected at the nucleotide sequence level. A sliding window analysis of sequences from the early regions of both phages revealed a substantial degree of similarity. Equally high scores, however, were found when the early region of Mu was compared to the late region of lambda and in self-comparisons of either Mu or lambda. Hence, the similarity is due to a common pattern of nucleotides rather than to sequence similarities between functionally related genes. Employing degenerated scoring matrices we could show that primarily adenine and thymine residues contribute to the high scores and that a specific clustering of these residues is the basis for the conserved pattern. Since such a similarity was not observed with control sequences of other phages. Escherichia coli or eukaryotic viruses, the data support the notion that Mu and lambda have diverged from a common phage module. In general, our approach could offer a simple and sensitive way to trace distant relationships.