This study aimed to explore the effects of removable aligners and fixed appliances on the supragingival bacterial communities in adult female patients undergoing orthodontic treatment. Supragingival plaque samples from 48 female individuals underwent microbiome analysis (16S rRNA gene sequencing) using PacBio Sequel sequencing. The study included 13 adults without orthodontic treatment needs as the control group (Group C), and 35 patients with comparable initial orthodontic conditions who received treatment at a university clinic in Beijing, China. The treatment involved either traditional fixed brackets (Group B, n = 17) or Invisalign® aligners (Group AT, n = 18). Bioinformatics methods were used for data analysis. From the 48 plaque samples, a total of 334,961 valid reads were obtained, averaging 6,978 sequences per sample. The 16S rDNA sequences were classified into 25,727 amplicon sequence variants (ASVs). Significant variances in alpha and beta diversity among the groups were noted. Group B microbiome exhibited an increased presence of Gram-negative bacteria. At the phylum level, Actinobacteriota was significantly more prevalent in Group C samples, while Bacteroidota was enriched in Group B samples. Family-level relative abundance analysis showed a notable increase in Saccharibacteria (formerly TM7) and Prevotellaceae in Group B. Genus-level analysis revealed a significant rise in Lautropia in Group AT. Fixed orthodontic appliances were linked to oral microbiome changes, notably an enhanced relative abundance of anaerobes, including periodontal pathogens. The observation points to the impact of orthodontic appliance on the oral microbial community, highlighting the difference between traditional braces (Group B) and clear aligners (Group AT)in terms of the predominance of anaerobic and gram negative bacteria. This emphasizes the importance of considering the microbiological effects when choosing orthodontic appliance and underscores the need for tailored oral hygiene practices for individuals undergoing these treatments. This research might provide insights that could assist in the development of innovative cleaning techniques and antibacterial materials.