Cetaceans are a mysterious group of secondarily-adapted marine mammals that “returned” from the land to the sea approximately 53–56 million years ago (Ma).  In order to adapt to dim aquatic environment, cetaceans have mostly rod photoreceptors and few cone photoreceptors, resulting in a loss of color vision. However, the genetic basis of visual degradation in cetaceans remains poorly explored. The GNAT2 and CNGB3 genes, expressed in cone photoreceptors play the key role in the phototransduction cascade. GNAT2 and CNGB3 genes of eight representative species of cetaceans were obtained by PCR amplified and gene downloaded from NCBI. Protein sequences of GNAT2 and CNGB3 were aligned by MEGA6.0. We found GNAT2 gene might become a pseudogene due to a 1-bp insertions at sites 148 and 1012 in Kogia sima and Physeter catodon, respectively. Similar results were indentified at

the CNGB3, with 1-bp deletions identified at sites 554 and 1407 of CNGB3 in P. catodon and apremature stop codon at site 1525-1527 in Balaenoptera acutorostrata. We predicted the three-dimensional (3D) structures of GNAT2 and CNGB3 using I-TASSER, and mapped the pseudogenized position onto the 3D structures. 3D structureal analysis showed that the insertion, deletion and premature stop codon were located in an important domain. Furthermore, branch model analysis revealed that relaxed selective pressure acted on cetacean lineages with pseudogenized GNAT2 and CNGB3. The pseudogenized GNAT2 and CNGB3 in cetacean lineages are suggested to be related to its deep diving and visual degradation to adapt completely aquatic environment. In addition, relaxed selection pressure of GNAT2 and CNGB3 was also detected in other cetacean lineages with increased ω values by free-ratio model, consistent with the morphological changes of eye for adapting to aquatic habitats.