AIM: To identify the spectrum and susceptibility pattern of isolated microorganisms from conjunctival flora of anophthalmic patients. METHODS: A cross-sectional clinical study including 60 patients with unilateral anophthalmia. Patients with use of antibiotic drops in their socket during the last month were also included. From each patient, three microbiological samples were taken from the lower conjunctival sac (healthy eye, pre-prosthesis, and retro-prosthesis space of socket). The 180 samples obtained were cultured. Isolates were identified and their antibiotic sensitivities were determined. RESULTS: A total of 251 isolates were recovered (62 isolates from healthy eye, 93 from pre-prosthesis, and 96 from retro-prosthesis space). The most common organism was Staphylococcus epidermidis, in both healthy eyes (64.5%) and sockets (45.5%). Altogether, coagulase-positive Staphylococci, Streptococci, and Gram-negative bacteria accounted for less than 15% of isolates in healthy eyes and more than 35% in sockets. Regarding the antibiotic sensitivities, there were no significant differences between isolates from sockets and healthy eyes. Nine patients recognized the use of self-prescribed antibiotic drops in their socket. In the healthy eyes of these subjects, Gram-positive microorganisms showed significantly greater resistance to aminoglycosides and tetracycline. CONCLUSION: Sockets of anophthalmic patients show a greater number of pathogens compared to healthy eyes. The use of antibiotic drops in the socket promotes a resistant flora not only in the socket but also in the healthy eye. Quinolones and macrolides may be better therapeutic options than aminoglycosides for treating conjunctivitis of anophthalmic sockets, since these antibiotics are less active against Staphylococcus epidermidis.