The oral ecosystem is strictly related to a balance maintained by specific niches recognized as sites, where oral bacteria can metabolize avoiding the immune system response. The oral bacteria species that colonize the ecological niches vary during fixed orthodontic treatment, with a prevalence of periodontal bacterial species. Qualitative analysis of five periodontal pathogens was used to investigate the microbial colonization rate in the crevice and buccal epithelial cells. The presence of inadequate oral hygiene was considered as a modulation variable for microbial colonization. Statistical analysis was performed by Fisher's exact test, ANOVA, and Pearson correlation. A P value lower than 0.05 was assumed as statistically significant. Tannerella forsythia was the only periodontal pathogen detected with a statistically admissible frequency. The positivity for Tannerella forsythia was correlated to sampling time and oral hygiene motivation. In buccal epithelial cells, both factors contributed to microbial decrease (P < 0.05), whereas, in crevice, oral hygiene motivation promoted a decrease in the microbial colonization rate (P < 0.05). According to microbiological findings, it is possible to identify how correct motivation for oral hygiene is more than enough to modulate or to avoid an upset of the oral ecosystem balance in early stages of orthodontic treatment.