Tonsillitis, characterized by inflammation of pharyngeal tonsils, is a common infection caused by a variety of viral or bacterial pathogens. This condition can manifest as acute, recurrent, or chronic tonsillitis, each posing distinct challenges for patients and healthcare systems. Recurrent and chronic forms, in particular, impose a significant healthcare burden due to their persistence and frequent relapses. An important factor contributing to the difficulties in treating recurrent and chronic tonsillitis is its relationship with biofilms—the structured microbial communities contained in the self-produced extracellular matrix. Biofilms provide great protection to bacteria, protect them from the host’s immune response, and reduce the effectiveness of antibiotics. Consequently, the treatment of these conditions often necessitates repeated courses of antibiotics, which not only strain healthcare resources but also exacerbate the global crisis of antimicrobial resistance. Among the pathogens implicated, Staphylococcus aureus and Streptococcus pyogenes are well-documented as biofilm-producing bacteria responsible for recurrent and chronic tonsillitis. Genetic factors play an important role in determining the susceptibility of people to recurrent tonsillitis. Variations in immune-related genes, particularly those involved in regulating immune responses, have been identified as key contributors. Understanding these genetic connections provides valuable insight into the pathophysiology of recurrent tonsillitis and highlights opportunities for individualized therapeutic strategies, such as targeted immunomodulatory therapies. Three major regulatory systems governing biofilm development have been identified: (i) quorum sensing, (ii) bis-(3′-5′)-cyclic diguanosine monophosphate, and (iii) small RNAs. Emerging research into biofilm dynamics and bacterial regulatory mechanisms offer promising directions for the development of more targeted therapeutic strategies. These advances have the potential to reduce reliance on antibiotics and invasive surgical interventions, enabling more effective and sustainable long-term solutions for managing chronic tonsillitis. A deeper understanding of these genetic and microbial mechanisms will be crucial for overcoming the limitations of current treatments and significantly improving patient outcomes.