The axolotl (Ambystoma mexicanum) has been a widely studied organism due to its capacity to regenerate most of its cells, tissues and whole-body parts. Since its genome was sequenced, several molecular tools have been developed to study the mechanisms behind this outstanding and extraordinary ability. The complexity of its genome due to its sheer size and the disproportionate expansion of a large number of repetitive elements, may be a key factor at play during tissue remodeling and regeneration mechanisms. Transcriptomic analysis has provided information to identify candidate genes networks and pathways that might define successful or failed tissue regeneration. Nevertheless, the epigenetic machinery that may participate in this phenomenon has largely not been studied. In this review, we outline a broad overview of both genetic and epigenetic molecular processes related to regeneration in axolotl, from the macroscopic to the molecular level. We also explore the epigenetic mechanisms behind regenerative pathways, and its potential importance in future regeneration research. Altogether, understanding the genomics and global regulation in axolotl will be key for elucidating the special biology of this organism and the fantastic phenomenon that is regeneration.