Some of the most important innovations in animal evolution were not driven by the evolution of new genes but instead resulted from changes in the regulation of conserved genes. These changes involve non-coding regulatory elements that are difficult to identify based on DNA sequence alone. However, potential regulatory sequences can be identified using a comparative evolutionary approach, searching for conserved non-coding elements (CNEs) that have been under purifying selection over large evolutionary time scales. Here, we conduct a large-scale characterization of CNEs across animal genomes. Using the k-mer based tool CNEfinder and a Python-based custom pipeline, we compared more than 50 metazoan genomes distributed among 16 animal phyla, resulting in more than 800 pairwise comparisons. For each comparison, we identify all sequences between 150 bp and 2 kb showing more than 90% sequence similarity. We have characterized the distribution of CNEs along chromosomes, annotated CNEs with their nearby genes, and scanned every CNE for known transcription factor binding sites. For each genomic dataset, we identified CNEs that remain in proximity with homologous genes across multiple species. We hypothesize that genes that ‘travel’ in close proximity to the same CNEs over large evolutionary time may be the transcriptional targets of these CNEs. Finally, we assess the distribution of each CNE on the animal tree to determine at which node they likely arose. We are currently using these data to identify candidate CNEs that may be involved in the evolution of taxon-specific traits.