Atypical mycobacteria are wide spread in the environment; they are now known to be a cause of a variety of infections including corneal infections especially after refractive surgery. The diagnosis and clinical management are often unsatisfactory due to misdiagnosis and requirement of prolonged combination of antibiotics. Evolving drug resistance is known to be a unique feature in managing atypical mycobacterial keratitis due to the propensity for the development of biofilms. In this article, we provide an etiology of atypical mycobacterial keratitis, mycobacterial biofilm pathogenesis, and the importance of mycobacterial biofilm matrix component (extracellular DNA) in maintaining mycobacterial biofilm matrix maintenance. Current treatment options for atypical mycobacterial keratitis are summarized and suggestions are made for the new treatment strategies targeting on the mycobacterial biofilm pathogenesis pathway.