This study aimed to establish the prevalence of non-pathogenic Neisseria spp. in urban and rural community in Cameroon and assess the antimicrobial susceptibility patterns. This cross-sectional study collected 629 oral rinse samples; 329 individuals from the urban University of Bamenda community and 300 inhabitants from the rural community of Santa, Cameroon between May to July 2024. A thousand-fold dilution of each sample was plated on selective media for growth of non-pathogenic Neisseria spp. with and without antibiotics. The prevalence of non-pathogenic Neisseria spp. within the study participants was 75.4% (474/629). The high prevalence was also observed within the different study site; 75.6% (249/329) in the University community and 75% (225/300) in Santa community. Non-pathogenic Neisseria species from the University community showed higher resistance rates to azithromycin (75.6%), ciprofloxacin (78.2%), and ceftriaxone (54,4%) than were recorded from Santa community; azithromycin (59.9%), ciprofloxacin (49.1%) and ceftriaxone (33.4%). The high prevalence of antibiotic resistance in non-pathogenic Neisseria spp. underscores the importance of understanding their potential role in spreading antimicrobial resistant genes.