Carps constitute one of the largest groups of lower vertebrates under teleosts and have emerged as the most important cultivable fishes. Rohu carp (Labeo rohita), belonging to family Cyprinidae, is one of the important aquaculture species accounting for about 2.5% of total freshwater aquaculture production worldwide. Cyprinid fishes have evolved physiological adaptations, with special characteristics, to suit to their habitats. Cypriniformes, along with Gymnotiformes, Characiformes and Siluriformes constitute a well known higher teleostean lineage, Otophysi which shares several common features among its members. One of them is auditory specialization with an accessory structure, Weberian ossicle connecting swim bladder and inner ear for superior peripheral hearing in this group of fishes. This special structure transmits oscillations of the swimbladder in a sound field to the inner ear thereby detecting sound at low levels and high frequencies by this group of fishes. We did compare the genomes of representative otophysan with non-otophysan species in order to identify putative genes/ clusters involved in the evolution of accessory auditory specialization. Comparative analysis of annotated genes between selected otophysan representatives and non-otophysans revealed 11572 orthologous clusters commonly shared by selected otophysans whereas 10126 clusters were shared by non-otophysans. Further, comparison between the core orthologous set from both otophysans and non-otophysans revealed 4963 gene clusters specific to otophysi and 3202 specific to non-otophysi. While looking into the GO term of the underlying gene clusters specific to otophysi, we identified several genes that are involved in pathways specific to multicellular organismal development, cartilages and bone differentiation, development of axial skeleton etc. The results of the present study can be a useful resource for studying genome evolution, and mechanisms of high capacity peripheral hearing systems in teleosts.