LAUSR

Ecosystems are interconnected networks of diverse habitat types, rather than isolated patches. However, the role of the multi‐habitat landscape in influencing microbial diversity remains poorly understood. This study investigates bacterial and fungal communities within a 2500‐year agricultural heritage system, the Mulberry‐dyke and Fish‐pond (MF), which integrates various terrestrial and aquatic habitats. Using amplicon sequencing, metagenomics, metatranscriptomics, and genomic analyses, these findings reveal a significant proportion of unclassified microbial taxa, underscoring the importance of MF systems as an untapped reservoir of microbial genetic resources. Moreover, single‐nucleotide‐level analyses demonstrate that a multi‐habitat landscape enhances microbial diversity through ecosystem‐wide assembly, facilitated by cross‐habitat microbial dispersal. Taxa found across multiple habitats exhibit convergence in microdiversity and adaptive genetic traits, indicating both ecological and functional mechanisms underlying their adaptability. A global analysis of public microbiome datasets furthermore confirms that regions with higher habitat heterogeneity support significantly higher taxonomic and functional diversity of microbiomes. Overall, this study sheds new light on the overlooked microbial diversity in traditional agricultural heritages and emphasizes the value of ancestral ecological wisdom underlying multi‐habitat integration for ecosystem management. These insights offer valuable guidance for developing sustainable agricultural strategies, enhancing microbial diversity, and reinforcing ecosystem resilience in the face of global change.