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Biofilms are present in more than 70% of endodontically diseased teeth. Through the advancements in the next-generation sequencing (NGS) technologies, microbiome research has granted a deeper analysis of the microbial communities living in human hosts. Here, we reviewed previous studies that used NGS to profile the microbial communities of root canals.A total of 12 peer-reviewed articles from PubMed were identified and critically reviewed. The study criteria were as follows: NGS platforms, sequenced bacterial hypervariable regions, teeth diagnosis with available patient information, sample characteristics, collection method, and microbial signatures.The most common NGS platforms used were 454 pyrosequencing (Roche Diagnostic Corporation, Risch-Rotkreuz, Switzerland) and Illumina-based technology (Illumina Inc, San Diego, CA). The hypervariable regions sequenced were between the V1 and V6 regions. The patient and sample population ranged from ages 12–76 years and asymptomatic and symptomatic teeth diagnosed with pulp necrosis with or without apical periodontitis. Microbial sampling was conducted directly from the infected pulp or the extracted teeth. The most abundant phyla were Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, and Fusobacteria. The most frequently detected genera were Prevotella, Fusobacterium, Porphyromonas, Parvimonas, and Streptococcus. Other notable microbial signatures at different taxa levels were identified but were widely variable between studies.Technologies based on high-throughput 16S ribosomal RNA NGS can aid in deciphering the complex bacterial communities of root canal biofilms. Thus far, only a few studies have been published with relatively small sample sizes, variable sample collection protocols, and community analyses methods. Future larger clinical studies are essential with validated standardized protocols for improved understanding of the pathogenic nature of bacterial biofilm communities in root canals.Polymicrobial communities are associated with endodontic diseases.Next-generation sequencing (NGS) offers deep coverage of microbial communities.Newer NGS provides improved accuracy and deeper coverage at reduced costs.NGS is useful for studying the microbiome of differing endodontic conditions.