Out of 112 corneal ulcers, which were clinically diagnosed as patients of microbial infections (fungal, bacterial, acanthamoeba and viral), attending the outpatient clinic and inpatient Ophthalmology Department of Tanta University Hospitals within 6 months (April – September, 2014), 43 cases were detected to possess fungal growth, and 46 cases were possessing bacterial infection according to results of microbial cultivation. All fungal and bacterial isolates were tested against the commercially available antimicrobial ophthalmic preparations (ofloxacin, moxifloxacin, gatifloxacin, tobramycin, ciprofloxacin for bacteria, ketoconazole, fluconazole, itraconazole, natamycin and voriconazole for fungi). Out of them 2 fungal isolates possessed 80% resistance to the tested antifungal agents, and 3 bacterial isolates gave 80% resistance to the tested antibiotics. All the 5 isolates were tested against 15 commercial essential oils (sage, anise, black seed, mustard, wheat germ, marjoram, jojoba, clove, chamomile, ginger, camphor, rosemary, watercress, parsley and gum oils). In case of fungal isolates, chamomile was the most effective oil against Aspergillus niger. The highest inhibition zone for bacterial isolate, identified later as Staphylococcus aureus, was recorded against rosemary. The antimicrobial action of the selected oils was highly observable and elucidated by TEM of both A. niger and S. aureus growth elements. Histopathological studies on the cornea of experimental animals revealed that the selected oils could be promisingly used in the treatment of resistant microbial keratitis.