Purpose: This study aimed to compare the compositional differences and functions of microbial communities in infected root canals of teeth with apical periodontitis (AP) and/or type 2 diabetes mellitus (T2DM) using 16S rDNA sequencing.Methods: Eighteen participants were categorized into two groups based on their health conditions: AP and AP complicated with T2DM (APDM). Infected root canal microbiota was clinically collected for 16S rDNA sequencing. Subsequent statistical and bioinformatics analyses were conducted after sequencing by NovaSeq, encompassing diversity analysis, intergroup difference analysis, and functional prediction analysis.The core microbiome of root canal microorganisms was similar in the two groups, which mainly consisted of Bacteroidota,