Background: (1) Periodontal disease (PD) is a globally prevalent chronic inflammatory condition, exacerbated by the dysbiosis of the oral microbiota. This study aims to evaluate the bacterial load of specific periodontopathogenic bacteria in patients with malocclusions (MAL) compared to those without. (2) Methods: Conducted at the “Carol Davila” University of Medicine and Pharmacy, Bucharest, Romania, this pilot study involved two groups: patients with MAL and PD, and patients with PD but without MAL. We included 20 patients: 10 with MAL (9 with crowding and 1 with an open bite) and 10 without MAL. Gingival crevicular fluid was collected for bacterial DNA extraction and quantified bacterial load using real-time PCR, focusing on 12 periodontopathogenic bacteria across different complexity classes. (3) Results: The study identified significantly higher concentrations of Treponema denticola (p = 0.023, median = 4.32, IQR = 2.76–5.53 vs. median = 1.93, IQR = 0–3.19), Tannerella forsythia (p = 0.020, mean = 6.04 ± 0.72 vs. mean = 4.4 ± 1.89) and Porphyromonas gingivalis (p = 0.002, median = 5.64, IQR = 4.94–5.98 vs. median = 2.48, IQR = 0–4.05) in patients with MAL compared to those without. This suggests that MAL contributes to an environment conducive to the proliferation of specific pathogens, potentially accelerating PD progression. Additionally, Eikenella corrodens (p = 0.040, mean = 4.55 ± 1.02 vs. mean = 3.23 ± 1.56), Campylobacter rectus (p < 0.001, mean = 4.2 ± 0.56 vs. mean = 1.8 ± 1.51), Prevotella intermedia (p = 0.043, median = 5.04, IQR = 0–5.49 vs. median = 0, IQR = 0–3.39), Capnocytophaga sputigena (p = 0.011, median = 5.91, IQR = 5.47–6.17 vs. median = 4.63, IQR = 3.83–5.64), and Capnocytophaga gingivalis (p = 0.007, median = 5.87, IQR = 5.34–6.03 vs. median = 4.4, IQR = 3.5–5.71) also showed elevated concentrations, indicating the broad impacts of MAL on oral microbial profiles. (4) Conclusions: The findings demonstrate a significant relationship between MAL and increased bacterial loads, underscoring the need for its integration in managing PD. Future research should expand demographic diversity and employ longitudinal designs to better understand the causative mechanisms at play.
