Urochordates are the closest relatives of vertebrates and at the larval stage, 
possess a characteristic bilateral chordate body plan. In vertebrates, the genes 
that orchestrate embryonic patterning are in part regulated by highly conserved 
non-coding elements (CNEs), yet these elements have not been identified in 
urochordate genomes. Consequently the evolution of the cis-regulatory code for 
urochordate development remains largely uncharacterised. Here, we use 
genome-wide comparisons between C. intestinalis and C. savignyi to identify 
putative urochordate cis-regulatory sequences. Ciona conserved non-coding 
elements (ciCNEs) are associated with largely the same key regulatory genes as 
vertebrate CNEs. Furthermore, some of the tested ciCNEs are able to activate 
reporter gene expression in both zebrafish and Ciona embryos, in a pattern that 
at least partially overlaps that of the gene they associate with, despite the 
absence of sequence identity. We also show that the ability of a ciCNE to 
up-regulate gene expression in vertebrate embryos can in some cases be localised 
to short sub-sequences, suggesting that functional cross-talk may be defined by 
small regions of ancestral regulatory logic, although functional sub-sequences 
may also be dispersed across the whole element. We conclude that the structure 
and organisation of cis-regulatory modules is very different between vertebrates 
and urochordates, reflecting their separate evolutionary histories. However, 
functional cross-talk still exists because the same repertoire of transcription 
factors has likely guided their parallel evolution, exploiting similar sets of 
binding sites but in different combinations.