The composition and functionality of opsin genes in a fish affect its visual capabilities and adaption to its habitat. Previously not many fish genomes were available and the changes in opsin gene sequences and copy number during fish evolution could not be fully revealed. We analyzed 46 fish genomes to study the genomic organization and evolution of opsin genes. We found that each round of whole genome duplication (WGD) had a strong effect on the syntenic organization of opsin gene-bearing loci and different opsin gene families experienced different kinds of changes. The tandem duplication was the most frequent duplication event that changed the opsin gene copy number in lineage-specific manner. Finally, we examined the evolution of key tuning sites in opsins in relation to the visual adaptation of fishes to different habitats such as epipelagic or demersal. Our study provides a detailed view of evolutionary changes in tuning sites, copy number and synteny of opsin genes in fishes and sheds light on the role of opsin genes in fine-tuning fish’s adaptation to diverse aqueous environments.