In this study we have described the detection of Bt gene and seed purity in maize by using PCR based method. Fifty four maize varieties were used for the detection of Bt gene by using BT1 and 35S primer having size of 195bp and 301bp respectively. Of these, fifteen varieties contained Bt gene which means that these varieties can not be used for further breeding. Ninety six seeds of maize were used for purity check by bnlg 161 SSR primer. Results showed that these seeds were 95% pure with 5% impurity. So these results showed that PCR based markers were very helpful in cultivar identification which leads to the improvement in maize breeding programs.