Identifying the mechanisms involved in the formation and maintenance of species is a central question in evolutionary biology and distinguishing the selective drivers of populations’ divergence from demographic processes is of particular interest to better understand the speciation process. Hybrid zones are recognized to provide ideal places to investigate the genetic architecture of speciation and to identify the mechanisms allowing diverging species to maintain their integrity in the face of gene flow. Here, we studied two alpine butterfly species in the genus Coenonympha: C. macromma and C. gardetta, which can be found flying together and hybridizing in narrow contact zones in the southern French Alps. We characterised the genomic composition of individuals, their morphology and their local habitat requirements, within and around a hybrid zone. Cline analysis showed that a significant portion of the genomic regions analysed were impermeable to introgression across a sharp hybrid zone (9 km wide), despite ongoing hybridisation between the species. We also found concordance between genetic, morphological and environmental variation across the hybrid zone, suggesting a coupling of different reproductive barriers. Habitat characteristics such as the presence of trees and shrubs and the start of the growing season were strongly associated with the genetic variation and we found evidence of genetic divergence at genetic markers associated with morphology and physiology, putatively involved in visual or environmental reproductive isolation. We discuss the various behavioural and ecological factors that might interplay to maintain current levels of divergence and gene flow between this species pair.