Allochrony is a form of reproductive isolation characterized by differences in the timing of breeding and may play a crucial role in the genetic and phenotypic divergence within species. This study explores the genetic and phenotypic divergence in Atlantic lumpfish (Cyclopterus lumpus), focusing on spring and autumn spawners along the Norwegian coast. Through genomic analysis and otolith morphology, we identified pronounced genetic and morphologic differences between the two spawning groups. Notably, chromosomes 13 and 14 exhibited local adaptations, while chromosome 1 showed parallel evolution across different localities, suggesting broader evolutionary processes influencing reproductive isolation and adaptive divergence. analysis revealed genes on chromosome 1 associated with responses to environmental stressors, possibly adaptations to seasonal variations at high latitudes. Morphological analysis of otoliths supported these findings, showing differences that may be adaptations to seasonal light availability. The presence of genomic islands of divergence, alongside a general lack of differentiation across the mitochondrial genome, suggests recent and rapid selection processes potentially moderated by ongoing gene flow. This study underscores the importance of considering temporal genetic structures in conservation and management strategies, particularly for species with bimodal spawning time to prevent overexploitation and optimize breeding programs.