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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. While research on COVID-19 has mainly focused on its epidemiology, pathogenesis, and treatment, studies on the naso-oropharyngeal microbiota have emerged in the last few years as an overlooked area of research. Here, we analyzed the bacterial community composition of the naso-oropharynx in 50 suspected SARS-CoV-2 cases (43 detected, 7 not detected) from Veraguas province (Panama) distributed across five age categories. Statistical analysis revealed no significant differences (<i>p</i> < 0.05) in bacterial alpha and beta diversities between the groups categorized by SARS-CoV-2 test results, age, or patient status. The genera <i>Corynebacterium</i>, <i>Staphylococcus</i>, <i>Prevotella</i>, <i>Streptococcus,</i> and <i>Tepidiphilus</i> were the most abundant in both detected and not-detected SARS-CoV-2 group. The linear discriminant analysis effect size (LEfSe) for biomarker exploration indicated that <i>Veillonella</i> and <i>Prevotella</i> were enriched in detected and hospitalized patients with SARS-CoV-2 relative to non-detected patients, while <i>Thermoanaerobacterium</i> and <i>Haemophilus</i> were enriched in non-detected patients with SARS-CoV-2. The results also indicated that the genus <i>Corynebacterium</i> was found to decrease in patients with detected SARS-CoV-2 relative to those with non-detected SARS-CoV-2. Understanding the naso-oropharyngeal microbiota provides insights into the diversity, composition, and resilience of the microbial community in patients with SARS-CoV-2.