The DNA of functional cis-regulatory modules displays extensive sequence conservation in comparisons of genomes from modestly distant species. Patches of sequence that are several hundred base pairs in length within these modules are often seen to be 80 -95% identical, although the flanking sequence cannot even be aligned. However, it is unlikely that base pairs located between the transcription factor target sites of cis-regulatory modules have sequence-dependent function, and the mechanism that constrains evolutionary change within cis-regulatory modules is incompletely understood. We chose five functionally characterized cis-regulatory modules from the Strongylocentrotus purpuratus (sea urchin) genome and obtained orthologous regulatory and flanking sequences from a bacterial artificial chromosome genome library of a congener, Strongylocentrotus franciscanus. As expected, singlenucleotide substitutions and small indels occur freely at many positions within the regulatory modules of these two species, as they do outside the regulatory modules. However, large indels (>20 bp) are statistically almost absent within the regulatory modules, although they are common in flanking intergenic or intronic sequence. The result helps to explain the patterns of evolutionary sequence divergence characteristic of cis-regulatory DNA.genomic sequence conservation ͉ indels ͉ regulatory evolution I n the general case where the transcription factor target sites are not known in advance, interspecific sequence comparison is now the method of choice for physically identifying putative cisregulatory modules in the intronic or intergenic DNA sequence of given animal genes. As has long seemed reasonable to assume on the grounds that they are functionally essential (1), these key regulatory units of the genome are evolutionarily conserved relative to flanking sequence. Thus, cis-regulatory modules can be detected computationally by interspecific comparison of the sequence surrounding the gene of interest, recognized as a block of sequence that has remained relatively similar between the two species, excised by PCR and incorporated in an expression vector. Their function can then be studied by direct gene transfer methods (e.g., refs. 2-12). The appropriate evolutionary species distance must be chosen: that is, not so close that unselected (i.e., ''background'') sequence has not had time to diverge but not so far that the pattern of conservation has been lost by too much divergence. But at the ''right'' distance, cis-regulatory modules stand out from the immediately flanking background as patches of well conserved sequence that are usually several hundred base pairs in length and terminated at their boundaries by abrupt transitions to sequence that has diverged too greatly for easy computational alignment.Despite its conventional rationale and remarkable practical usefulness, there has remained a deeply problematic aspect of the conservation of cis-regulatory module DNA. Cis-regulatory modules consist of clusters of transcription factor ...