Intrusion detection systems detect attacks inside computers and networks, where the detection of the attacks must be in fast time and high rate. Various methods proposed achieved high detection rate, this was done either by improving the algorithm or hybridizing with another algorithm. However, they are suffering from the time, especially after the improvement of the algorithm and dealing with large traffic data. On the other hand, past researches have been successfully applied to the DNA sequences detection approaches for intrusion detection system; the achieved detection rate results were very low, on other hand, the processing time was fast. Also, feature selection used to reduce the computation and complexity lead to speed up the system. A new features selection method is proposed based on DNA encoding and on DNA keys positions. The current system has three phases, the first phase, is called pre-processing phase, which is used to extract the keys and their positions, the second phase is training phase; the main goal of this phase is to select features based on the key positions that gained from pre-processing phase, and the third phase is the testing phase, which classified the network traffic records as either normal or attack by using specific features. The performance is calculated based on the detection rate, false alarm rate, accuracy, and also on the time that include both encoding time and matching time. All these results are based on using two or three keys, and it is evaluated by using two datasets, namely, KDD Cup 99, and NSL-KDD. The achieved detection rate, false alarm rate, accuracy, encoding time, and matching time for all corrected KDD Cup records (311,029 records) by using two and three keys are equal to 96.97, 33.67, 91%, 325, 13 s, and 92.74, 7.41, 92.71%, 325 and 20 s, respectively. The results for detection rate, false alarm rate, accuracy, encoding time, and matching time for all NSL-KDD records (22,544 records) by using two and three keys are equal to 89.34, 28.94, 81.46%, 20, 1 s and 82.93, 11.40, 85.37%, 20 and 1 s, respectively. The proposed system is evaluated and compared with previous systems and these comparisons are done based on encoding time and matching time. The outcomes showed that the detection results of the present system are faster than the previous ones.