When two symbolic representations of DNA or protein sequences are arranged next to one another so that their most similar elements are juxtaposed they are said to be aligned. Many bioinformatics tasks depend upon successful alignments. Alignments are conventionally shown as traces. In this research work we try to find out the molecular sequence similarity of Culex quinquefasciatus - multidrug resistance protein using bioinformatics techniques. The results obtained from our current researh explain how the Culex quinquefasciatus - multi drug resistance protein is molecularly related to Aedes aegypti species. We also represent the molecular functional part of the target protein sequences in culex and aedes species. In future, the same chemical compounds can be used to inhibit the protein targets of the two species using Cheminformatics studies.