Cichlids fishes exhibit extensive phenotypic diversification and speciation. Encounters with new environments alone are not sufficient to explain this striking diversity of cichlid radiation because other taxa coexistent with the Cichlidae demonstrate lower species richness. Wagner et al analyzed cichlid diversification in 46 African lakes and reported that both extrinsic environmental factors and intrinsic lineage-specific traits related to sexual selection have strongly influenced the cichlid radiation 1 , which indicates the existence of molecular mechanisms responsible for rapid phenotypic diversification and events leading to reproductive isolation. However discovery of the molecular mechanisms in terms of genetic or transcriptomic or proteomic diversity responsible for the rapid speciation in a short geological time has remained elusive. In this study we integrated transcriptomic and proteomic signatures from two cichlids species, identified novel open reading frames (nORFs) and performed evolutionary analysis on these nORF regions. Our results suggest that the time scale of speciation of the two species can be better explained by the evolutionary divergence of these nORF genomic regions. Therefore this study has revealed the potential functional and evolutionary role of nORFs, which has far reaching implications for such evolutionary and speciation studies that have traditionally been focussed on known protein coding regions.