Ultra-conserved sequence elements in vertebrate enhancers suggest that fundamental gene regulatory mechanisms are shared across phylogenetically diverse species. Our previous studies took advantage of the availability of the assembled genomic sequences of the Mediterranean fruit fly Ceratitis capitata, the domestic housefly Musca domestica, and Drosophila to explore the integrity of regulatory sequences across the ~100 million years of divergence between these dipterans. We have shown that many of the conserved sequence blocks (CSBs) that constitute Drosophila enhancers, identified using the multispecies alignment algorithm EvoPrinter, are often nearly completely conserved in both Ceratitis and Musca. Analysis of the linear positioning of these CSBs with respect to the associated structural genes is also conserved. Availability of the genomic sequence the bumble bee Bombus impatiens, honey bee Apis mellifera and the European bee Megachile rotundata reveals conserved sequence elements bearing strong structural resemblance to those found in flies. Surprisingly, alignment of regulatory sequences from bee species with those of 10 ant species, representing two families of social insects of the order Hymenoptera, revealed widespread alignment of the bee sequences with orthologous ant sequences. These alignments also revealed bee- and ant-specific sequences intermingled with CSBs common to both taxa. We conclude that comparison across ant and bee species reveals ultra-conserved enhancers that bear taxa specific sequence modifications. These studies allow for a greater understanding of enhancer evolution and constitute a first step in the comparative analysis of gene regulation in these species.