The ecosystem of coastal lakes influences the prevalence of halophilic organisms, leading to significant changes in the microbial community structure, with the emergence of distinct extremophile microbes. Gili Meno Lake serves as a human reservoir on Gili Meno Island. We utilize long-read metagenomics to explore the microbial diversity of Gili Meno Lake to contribute in the future microbial prospect and sustainably managing these critical resources.