Aim: To study bacterial conjunctival flora before and after topical moxifloxacin or besifloxacin used as prophylactic agent in intraocular surgeries. Settings and design: Prospective randomized study. Material and methods: Conjunctival swabs of 100 patients undergoing intraocular surgeries were collected 2 days before the surgery without prior antibiotic use and inoculated on culture media for culture and antibiotic sensitivity tests. Patients were randomized into two groups (50 each). Patients of Group A and Group B received topical moxifloxacin 0.5% and besifloxacin 0.6% eye drop, respectively, to the assigned eye 6 hourly. Postoperatively, antibiotic eye drops were instilled 4 hourly for 10 days and then stopped. Topical anti-inflammatory and steroid drugs were continued for 6 weeks. Conjunctival swabs were repeated from operated eyes 20 and 40 days postoperatively. Statistical analysis was done using Chi-square and McNemar’s tests. Results: Bacterial growth appeared in 27 cases (most commonly Staphylococcus epidermidis 51.85%) - 16 in Group A and 11 in Group B - and none of the isolate showed resistance to the assigned antibiotic. Conclusions: The antibacterial efficacy of topical moxifloxacin and besifloxacin in preventing postoperative infections is similar; hence, both may be equally effective for prophylaxis in intraocular surgeries.