Pesticides are used widely in the agriculture industry to control various types of pests but at the same time, their extensive applications have caused both environmental and public health concerns. Usually the genetic toxicities of pesticides are determined by several factors, such as their bioaccumulation or persistence in the environment, their metabolism in humans and their reactivity with cellular bimolecules such as DNA, RNA and proteins. Hence, genotoxicity evaluation of such chemical has become basic requisite before their enormous application on agricultural products. In relevance to this, the present topic of research deals with genotoxicity assessment of ethion at molecular level by exposing genome of Culex quinquefasciatus to LC20 of concerned chemical for 24 hours. The rDNA ITS1 sequence of treated and control samples were amplified by using forward and reverse primers having nucleotide sequence FP 5 ´-C C T T T G T A C A C A C C G C C C G T-3´ and RF 5 ´-G T T C A T G T G T C C T G C A G T T C A C-3´ respectively. Amplified products were sequenced and subsequentlyaligned with help of Clustal W software programme. A total of 321 different types of alterations were detected in rDNA ITS1 sequences obtained from ethion treated stocks which included 41 insertions, 48 deletions, 111 transitions and 121 transversions. According to these values it was evident that maximum numbers of errors were in the form of transversions while insertions were minimum. Furthermore, it was observed that in ethion treated individuals a decrease in GC content and an increase in AT content were observed as compared to controls.