Microbial communities are complex networks of microorganisms that interact with each other and their environment. Understanding the functional roles of individual species and their interactions is challenging. High-throughput sequencing has provided valuable insights into microbial communities, but the vast amounts of data generated make deciphering mechanisms difficult. Gene regulatory networks (GRNs) provide a powerful framework for studying the functional roles of individual genes and their interactions in complex biological systems. In microbial ecology, GRNs can be used to identify key regulatory genes and their targets involved in ecological processes. By integrating genomic and transcriptomic data with environmental metadata, GRNs can reveal the genetic architecture of microbial communities. This review provides an overview of the application of GRNs in microbial ecology and discusses the challenges and opportunities of using this approach. Case studies demonstrate the potential of GRNs in uncovering novel insights into microbial community structure and function. Integration of GRNs with other omics approaches and environmental metadata holds great promise in advancing our understanding of microbial ecology and its relevance to human health and environmental sustainability.