Aedes aegypti is a mosquito that can spread the dengue fever, Chikungunya and yellow fever viruses, and other diseases. The mosquito can be recognized by white markings on legs and a marking in the form of a lyre on the thorax. The mosquito originated in Africa but is now found in tropical and subtropical regions throughout the world. Culex quinquefasciatus is the vector of lymphatic filariasis caused by the nematode Wuchereria bancrofti in the tropics and sub tropics. The present research investigation studies primarily focus on the molecular similarities of Aedes aegypti and Culex quinquefasciatus. Our aim is to reduce the pathological effects of dengue and filarial disease in humans. The molecular sequence alignment is one of the best drug targets for structure based drug designing. The protein functional similarities identification using advanced motif prediction tool MEME. We finally conclude from the results that the identified conserved motif sequences are the potential protein target sequences for structure based drug designing and molecular drug docking studies. This work would definitely be useful in the field of Clinical Pathology, Computational Entomology and Cheminformatics.