This study aimed to identify trends in bacteria isolated from Korean adults with chronic rhinosinusitis (CRS). Enrolled were CRS patients who underwent sinus bacterial culture during endoscopic sinus surgery between 2007–2008, 2011–2012, and 2017–2018 (n = 510). Patients’ clinical characteristics, bacterial culture results, and antibiotic resistance were reviewed. The bacteria isolation rate was 76.3% (73.9% for CRS with nasal polyps and 82.8% for CRS without nasal polyps; p = 0.038). In total, 650 strains were isolated, the most common was Coagulase Negative Staphylococci (CNS) (28.0%), followed by Streptococcus species (12.2%), Propionibacterium species (8.0%), Corynebacterium species (7.5%), Staphylococcus aureus (6.2%), Haemophilus species (5.7%), Klebsiella species (5.1%), and Pseudomonas aeruginosa (4.2%). Furthermore, an analysis of the bacterial trends in the three groups showed significant increases over time for the isolation of CNS (p = 0.006), Klebsiella (p = 0.002), and P. aeruginosa (p = 0.007) and extended-spectrum beta-lactamase (ESBL) producing Klebsiella (p < 0.001) and Enterobacter (p = 0.007) species in terms of antibiotics resistance. This study demonstrates that the frequency of CNS, Klebsiella, and P. aeruginosa in CRS patients and the ESBL-producing Klebsiella and Enterobacter species has significantly increased in CRS patients over the last decade.