The purpose of the microbial diversity studies conducted is to discover species composition, structure, bacterial distribution, spatial activity as well as the function and role of the microbial. A laboratory-scale sequencing batch reactor with a working volume of 2 L was used to develop aerobic granular sludge to treat livestock wastewater. The seed sludge was taken from municipal wastewater treatment plant, while the wastewater was collected from cattle farm at Primaternak Enterprise, Johor, Malaysia. The composition and diversity of microbial community in the seed sludge and aerobic granules were explored using next generation sequencing analysis. Based on the findings, the details of phylogenetic bacterial which consists of phylum, class, order and family were identified and compared between the seed sludge and aerobic granules. The metagenome DNA sequencing analysis has revealed an abundance of microbial diversity in the seed sludge and 8 hours aerobic granular sludge samples. The metagenome analysis discovered wide variety of microorganism including archaea, bacteria, eukaryote, and virus. Bacteria has been evaluated as the most dominant microbial in both seed sludge and aerobic granules. Acidovorax sp JS42 was found to be the most abundance bacteria species in seed sludge while Thauera MZIT was the most abundance bacteria species in aerobic granules. Whereas, Bacteroides, Flavobacterium, Comamonas, Pseudomonas and Acinetobacter were the most abundance bacteria that responsible in developing aerobic granules were observed to be higher in aerobic granules compared to the seed sludge. The results from this study indicated that distinct differences of microbial community from the seed sludge and aerobic granular sludge were observed clearly, which provided some evidence of the granulation process.