Background This study analyzed the levels of a specific group of periodontal health/disease‐related oral bacteria in the subgingival biofilm of young adults with overweight (OW) and obesity (OB), and no destructive periodontal disease. Methods Full‐mouth periodontal assessment and subgingival biofilm sampling were performed in individuals with normal weight (NW) (BMI body mass index ≥18.5 to ≤24.9 kg/m2; n = 29), OW (BMI ≥25 to ≤29.9 kg/m2; n = 26), or OB (BMI ≥30 kg/m2; n = 22). BMI, waist (WC) and hip (HC) circumferences, and waist‐hip ratio (WHR) were established for every individual. Biofilm samples were analyzed by checkerboard. Spearman coefficient, linear, and logistic regression analyses were obtained. Results Gingivitis was detected in 45% NW, 65% OW, and 73% OB individuals. NW patients presented significantly less calculus and supragingival biofilm than OB. OW, and OB individuals had significantly higher levels of Porphyromonas gingivalis and Tannerella forsythia than NW patients (P <0.05). Treponema denticola correlated with BMI (rho = 0.31), WC (rho = 0.28), and HC (rho = 0.29), P≤0.01. Linear regression analysis showed significant (P <0.05) positive associations between BMI, WC, HC, and WHR indicators and Prevotella spp., Lactobacillus spp., V. parvula, and A. actinomycetemcomitans (Aa); negative associations were found between Capnocytophaga spp., WC, and HC (β = −0.29 and β = −0.37, respectively; P <0.01). However, the interaction of Prevotella spp. and T. forsythia decreased the likelihood of an individual to be diagnosed as OW/OB (OR 0.183 95% CI, 0.062–0.540). Conclusions Few periodontal pathogens differed in levels between NW and OW/OB individuals without destructive periodontal disease. Moreover, Aa, T. denticola, and Prevotella spp. were associated with clinical parameters of obesity.