The present investigation is attributed to genotoxicity assessment of a carbamate pesticide carbaryl, at nucleotide level by comparing rDNA ITS1 sequence of treated groups with control stocks. To achieve objective, second instar larvae of Culex quinquefasciatus were exposure to LC20 of carbaryl for duration of 24 hours. The detrimental consequences of concern pesticide, were analyzed after in vitro amplification of rDNA ITS1 by polymerase chain reaction technique using specific forward and reverse primers having sequence of FP 5 '-C C T T T G T A C A C A C C G C C C G T-3 ' and 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. Subsequently to sequence alignment with clustalW software, various alterations in form of additions, deletions, transitions and transversions were observed in pesticide treated samples. During present research about 390 alterations were detected in pesticide exposed groups, comprised 18 additions, 58 deletions, 142 transitions and 172 transversions of bases. Furthermore, carbaryl possess tendency to induced maximum deletions of adenine base and maximum addition of thymine nucleotide. In case of transitions and transversions, carbaryl had a maximum potential of affecting the guanine base.