Purpose We compared the resistance patterns of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible Staphylococcus aureus (MSSA) keratitis isolates to common topically applied ophthalmic antimicrobials. Methods We reviewed the antibiotic susceptibility results of 122 MRSA and 276 MSSA keratitis isolates from January 1993 to November 2012. In vitro susceptibility testing of each SA isolate was performed using Kirby-Bauer disk diffusion based on modified serum interpretations for cefoxitin, bacitracin, cefazolin, ciprofloxacin, gatifloxacin, gentamicin, moxifloxacin, ofloxacin, polymyxin B, sulfamethoxazole, tobramycin, and trimethoprim. Results MRSA represented 30.7% (122 of 398) of the total SA isolates. All SA isolates were susceptible to vancomycin, while less susceptible to the fluoroquinolones than to the non-fluoroquinolones. In comparison to MSSA, MRSA was significantly more resistant to all antibiotics tested other than polymyxin B (both equally resistant) and vancomycin (both equally susceptible) (p<0.001). Besides vancomycin, MRSA demonstrated the best susceptibilities to sulfamethoxazole (94.3%), bacitracin (89.3%), trimethoprim (88.5%), and gentamicin (86.1%). Additionally, MRSA was found to be significantly more resistant to the second-generation fluoroquinolones (ciprofloxacin and ofloxacin) than to the fourth-generation fluoroquinolones (moxifloxacin and gatifloxacin). An increase in resistance to the fourth-generation fluoroquinolones was detected for both MRSA and MSSA over the study period. Conclusions The in vitro susceptibilities of commonly used topical antibiotics differ for MRSA and MSSA isolates, thus successful treatment of bacterial keratitis should be supported with laboratory studies. Vancomycin remains the treatment of choice for MRSA keratitis. The empiric use of second-generation fluoroquinolones appears to be contraindicated in the treatment of MRSA keratitis.