Background: Ear infections rank among the most common health presentations in children attending clinics in Iraq and their microbiology continues to evolve. Staphylococcus epidermidis has transitioned from being disregarded as an innocuous commensal organism to a creeping opportunist drug-resistant pathogen, primarily due to its prolific biofilm-forming ability enabling the establishment of chronic and recurrent otitis media that are significantly more resistant to eradication. Objectives: The aim of this study was to identify the prevalence of S. epidermidis, evaluate biofilm genes carriage (icaA/icaD) and their associated factors among children with otitis media in Al-Diwaniyah. Methods: A total of 120 afresh suffering children age between 5-10 years with clinically diagnosed otitis media were enrolled in hospitals through the period between January and May 2024 in Al Diwaniyah City. Swab from the ear were cultured on blood agar and mannitol salt agar. Identification of isolates was performed by standard methods and confirmed with API Staph. Tubes were tested by PCR for icaA and icaD, and disk diffusion was performed to determine antibiotic susceptibility according to CLSI 2024. Results: Staphylococcus epidermidis was isolated from 76 out of the 120 children (63.3%). The predominant risk factor was poor nail hygiene; children with dirty nails had a much higher culture positivity (82.1% vs. 45.5%; OR = 5.42, 95% CI: 2.38–12.35, p <0·001). Bilateral ear involvement was also positively associated (p = 0.012). Conclusion: Staphylococcus epidermidis is an important pathogen in the pediatric otitis media in Al Diwaniyah and must be more than a contaminant. The close link with the bad hygiene of nails gives a very inexpensive and educable form of prevention for the ones who care for it. In addition, our antimicrobial data show that empirical penicillin therapy would otherwise be futile. Thus, it will be recommended that either ciprofloxacin or gentamicin is preferred concerning to the empirical therapy while waiting for definitive culture products.