Adaptation to arboreal environments requires overcoming gravitational constraints, driving repeated morphological innovations across snake lineages. Among these, elongated tails represent a key adaptation that enhances branch-gripping ability, yet the genomic changes underlying this trait remain poorly understood. Here, ancestral state reconstruction revealed that arboreality evolved independently in multiple snake clades, with tail elongation as a recurrent morphological adaptation. To investigate its genetic underpinnings, we generated a high-quality, chromosome-level genome assembly for the green cat snake (Boiga cyanea) and performed comparative analyses with the Asian vine snake (Ahaetulla prasina). We identified accelerated evolution in genes associated with somite specification, a critical process for axial elongation, and detected positive selection in key somitogenesis regulators, including HES7 and TBX18. Notably, LOXL3, which contributes to somite boundary formation, exhibited a conserved amino acid substitution in both arboreal lineages. In addition, convergent divergence of conserved nonexonic elements (CNEs) was observed in genomic regions linked to the GDF11-LIN28-HOX13 pathway, which governs the axial-to-tail transition. Functional assays confirmed that divergence in these CNEs alters regulatory activity, potentially modulating gene expression within critical developmental pathways. Collectively, our findings establish a genomic framework for snake axial elongation, highlighting how arboreal specialization shaped tail length evolution.