Chronic rhinosinusitis (CRS) is defined as an inflammatory disorder of the paranasal sinuses and of the nasal mucosa that lasts 12 weeks or longer. In CRS microbes contribute to the disease pathogenesis. Clinical microbiology is focused on finding single pathogens that causes the disease and the main goal is the use of antibiotics to kill bacteria. Efforts to achieve a better understanding of CRS include the study of the sinus microbiome, and to evaluate the ability of probiotics to augment homeostasis and modulate the immune response of the host mucosa. This review provides an update on the role of the microbiome in CRS. The study was conducted using two databases: PubMed and Science Direct. We searched for articles in English that matched the review topic. We first used the abstracts of articles to assess whether they met the inclusion criteria. We also reviewed the references of the selected articles and read those with titles that might be of interest. Several studies have shown that endogenous microbiome dysbiosis can impact mucosa health and disease severity. Some bacterial species presenting protective or pathogenic effect. Antimicrobial agents can create a similar disruption and impact the nasal microbiome balance. On the other hand, probiotics offers a promising avenue for developing systemic and topical therapies geared towards strategic manipulation of the biological host load, thereby augmenting immune homeostasis. A better comprehension of sinus-nasal microbiome in healthy and in CRS patients and the link with different CRS phenotype can help in developing new prognostics, diagnostics, and therapeutics strategies. Going forward, the use of probiotics can restore the native sinus ecology with significant therapeutic and preventive implications.