Undoubtedly, diagnosing and managing infections is one of the most challenging issues for orofacial clinicians. As a result of the diversity of symptoms, complicated behavior, and sometimes confusing nature of these conditions, it has become increasingly difficult to diagnose and treat them. It also highlights the need to gain a deeper insight into the orofacial microbiome as we try to improve our understanding of it. In addition to changes in patients’ lifestyles, such as changes in diet, smoking habits, sexual practices, immunosuppressive conditions, and occupational exposures, there have been changes in patients’ lifestyles that complicate the issue. Recent years have seen the development of new infection treatments due to the increased knowledge about the biology and physiology of infections. This review aimed to provide a comprehensive overview of the types of infections in the mouth, including the types that viruses, fungi, or bacteria may cause. It is important to note that we searched the published literature in the Scopus, Medline, Google Scholar, and Cochran databases from 2010 to 2021 using the following keywords: “Orofacial/Oral Infections,” “Viral/Fungal/Bacterial Infections”, “Oral Microbiota” And “Oral Microflora” without limiting our search to languages and study designs. According to the evidence, the most common infections in the clinic include herpes simplex virus, human papillomavirus, Candida albicans, Aspergillus, Actinomycosis, and Streptococcus mutans. The purpose of this study is to review the new findings on characteristics, epidemiology, risk factors, clinical manifestations, diagnosis, and new treatment for these types of infectious diseases.