Uncertain atmosphere is a prevalent factor affecting the existing prediction approaches. Rough set and fuzzy set theories as proposed by Pawlak and Zadeh have become an effective tool for handling vagueness and fuzziness in the real world scenarios. This research work describes the impact of Hybrid Intelligent System (HIS) for strategic decision support in meteorology. In this research a novel exhaustive search based Rough set reduct Selection using Genetic Algorithm (RSGA) is introduced to identify the significant input feature subset. The proposed model could identify the most effective weather parameters efficiently than other existing input techniques. In the model evaluation phase two adaptive techniques were constructed and investigated. The proposed Artificial Neural Network based on Back Propagation learning (ANN-BP) and Adaptive Neuro Fuzzy Inference System (ANFIS) was compared with existing Fuzzy Unordered Rule Induction Algorithm (FURIA), Structural Learning Algorithm on Vague Environment (SLAVE) and Particle Swarm OPtimization (PSO). The proposed rainfall prediction models outperformed when trained with the input generated using RSGA. A meticulous comparison of the performance indicates ANN-BP model as a suitable HIS for effective rainfall prediction. The ANN-BP achieved 97.46% accuracy with a nominal misclassification rate of 0.0254%.