It is well documented that gene regulatroy networks can evolve extensively through mutations to cis-regulatory modules. Transcription factor proteins that bind these cis-regulatory modules may also evolve to produce novelty. Such coding changes, however, are considered to be more rare, because transcription factors are highly pleiotropic and hence are more constrained to evolve in ways that will not produce widespread detrimental effects. Recent technological advances have unearthed a surprising variation in DNA-binding abilities, such that individual transcription factors may recognize both a preferred primary motif and an additional secondary motif. This provides a source of modularity in function. In this talk, we will present recent work that shows that orthologous transcription factors can also evolve a changed preference for a lower affinity secondary binding motif, thereby offering an unexplored mechanism for GRN evolution. We demonstrate that this difference may allow for greater evolutionary change in timing of regulatory control and provide a mechanism through which organisms can evolve a changed response to signaling gradients. This uncovers a layer of transcription factor binding divergence that could exist for many pairs of orthologs and provides a mechanism through which transcription factors can evolve to produce subtle changes in phenotype.