Breast cancer harbors a distinctive microbial community that significantly differs in quantity and diversity from normal breast tissue, benign breast diseases, and adjacent non-cancerous tissues. Moreover, the microbial composition varies among different molecular subtypes, grades, and stages of breast cancer, which are pivotal for clinical prognosis and therapeutic decision-making. This suggests a pivotal role for the breast cancer-associated microbiota in the initiation, progression, and treatment of breast cancer. Nevertheless, studies in this field have been influenced by factors such as ethnic and geographical disparities, sample sizes, and sequencing depths, leading to variations in research outcomes and an absence of comprehensive reviews. Therefore, this paper summarizes the latest research progress of microbiota sequencing in breast cancer, systematically analyzes the differences in microbial composition between breast cancer tissues and non-cancerous tissues, and between different molecular subtypes, pathological grades and stages of breast cancer, and looks forward to and discusses the roles of microbiota in the diagnosis and treatment of breast cancer, with the aim of providing a new perspective for the future diagnosis and treatment of breast cancer based on microbiota.