Developmental genes are regulated by complex, distantly located cis-regulatory 
modules (CRMs), often forming genomic regulatory blocks (GRBs) that are 
conserved among vertebrates and among insects. We have investigated GRBs 
associated with Iroquois homeobox genes in 39 metazoans. Despite 600 million 
years of independent evolution, Iroquois genes are linked to 
ankyrin-repeat-containing Sowah genes in nearly all studied bilaterians. We show 
that Iroquois-specific CRMs populate the Sowah locus, suggesting that regulatory 
constraints underlie the maintenance of the Iroquois-Sowah syntenic block. 
Surprisingly, tetrapod Sowah orthologs are intronless and not associated with 
Iroquois; however, teleost and elephant shark data demonstrate that this is a 
derived feature, and that many Iroquois-CRMs were ancestrally located within 
Sowah introns. Retroposition, gene, and genome duplication have allowed 
selective elimination of Sowah exons from the Iroquois regulatory landscape 
while keeping associated CRMs, resulting in large associated gene deserts. These 
results highlight the importance of CRMs in imposing constraints to genome 
architecture, even across large phylogenetic distances, and of gene 
duplication-mediated genetic redundancy to disentangle these constraints, 
increasing genomic plasticity.