The evolution of transcriptional regulatory mechanism is central to how stress response and tolerance differ between species. However, it remains largely unknown how divergence in cis-regulatory sites and, subsequently, transcription factor (TF) binding specificity contribute to stress-responsive expression divergence, particularly between wild and domesticated species. By profiling wound-responsive gene transcriptomes in wild Solanumpennellii and domesticated S. lycopersicum, we found extensive wound-response divergence and identified 493 S. lycopersicum and 278 S. pennellii putative cis-regulatory elements (pCREs) that were predictive of wound-responsive gene expression. Only 24-52% of these wound response pCREs (depending on wound-response patterns) were consistently enriched in the putative promoter regions of would-responsive genes. In addition, between these two species, their differences in pCRE site sequences were significantly and positively correlated with differences in wound-responsive gene expression. Furthermore, ~11-39% of pCREs are specific to only one of the species and likely bound by TFs from different families. These findings indicate substantially regulatory divergence in these two plant species diverged ~3-7 million years ago. Our study provides new insights into the mechanistic basis of how the transcriptional response to wounding is regulated and, importantly, the contribution of cis-regulatory components to variation in wound-responsive gene expression between a wild and a domesticated plant species.