Recent advancements in Software Defined Networking (SDN) makes it possible to overcome the management challenges of traditional network by logically centralizing control plane and decoupling it from forwarding plane. Through centralized controllers, SDN can prevent security breach, but it also brings in new threats and vulnerabilities. Central controller can be a single point of failure. Hence, flow-based anomaly detection system in OpenFlow Controller can secure SDN to a great extent. In this paper, we investigated two different approaches of flow-based intrusion detection system in OpenFlow Controller. The first of which is based on machine-learning algorithm where NSL-KDD dataset with feature selection ensures the accuracy of 82% with Random Forest classifier using Gain Ratio feature selection evaluator. In the later phase, the second approach is combined with Gated Recurrent Unit Long Short-Term Memory based intrusion detection model based on Deep Neural Network (DNN) where we applied an appropriate ANOVA F-Test and Recursive Feature Elimination feature selection method to improve the classifier performance and achieved an accuracy of 88%. Substantial experiments with comparative analysis clearly show that, deep learning would be a better choice for intrusion detection in OpenFlow Controller.