Oral immunity is an essential barrier for protection against pathogens, supporting oral health, and overall health-related challenges. Nevertheless, dysregulation of oral immunity results in different pathological conditions that are often challenging to diagnose and manage. Biomarkers have revolutionized the management of oral health by offering information about molecular and cellular immune events, disease etiology, and treatment outcomes. This review focuses on the biomarkers for oral immunity in the context of the existing trends and includes genetic, proteomic, metabolomic, and microbiome biomarkers. Single-nucleotide polymorphism (SNP) and copy number variation (CNV) have improved the knowledge of the genetic risk factors for oral diseases and the treatment plan for patients. Cytokines, matrix metalloproteinases (MMPs), and antimicrobial peptides (AMPs) have enhanced the diagnostic accuracy of diseases, prognostication, and evaluation of therapeutic efficacy. Metabolomic biomarkers have provided valuable insights into the biochemical pathways related to oral health and diseases, while microbiome-derived biomarkers have revealed the intricate host-microbiota interactions. Recent developments in high-throughput screening, multi-omics, and computational biology have facilitated the identification of biomarkers of oral immunity. These molecular markers have been proven to have the potential for screening, prognosis, and targeted therapy of oral diseases such as periodontitis, oral cancer, and autoimmune diseases. However, some issues are still to be solved, such as standardization of biomarker usage, obtaining the approval of biomarkers by different authorities, and the economic issues regarding the application of biomarkers for clinical diagnostics.