show Abstracthide AbstractEuropean green lizards are terrestrial lizards spread across Europe occupying areas with dense vegetation. Their populations are currently declining due to habitat loss, some regions have legislated protection laws for their conservation. L. viridis (eastern green lizard) and L. bilineata (western green lizard) are sister-species which were until recently were grouped together as the L. viridis complex (European green lizards). These two species occupy distinct geographical niches and are known to have recently diverged. We sequenced, assembled and compared their genomes to understand the main factors contributing to the divergent evolution of European green lizards.