PCR is rapid diagnostic technique to detect the infectious agents even in small volume of samples. PCR is typically used when the patient’s natural history does not coincide with his or her clinical presentation or when a patient does not respond appropriately to therapy. Ophthalmic samples for PCR are collected in three ways; the samples are corneal scraping, intraocular fluids and infected ocular tissues. All samples are collected by swabbing, scrapping and/or an anterior chamber paracentesis. Once obtained the specimens should be quick-frozen on dry ice or in liquid nitrogen and should remain so until the laboratory receives the sample. PCR consists of three important steps which are DNA extraction, amplification of the extracted DNA by PCR and analysis of the amplified products by agarose gel electrophoresis. Primers used for identification of ocular fungal genome are the Internal Transcribed Spacer Region (ITS1 and ITS4). The PCR reaction is carried out in a 50 ml reaction volume with 5 ml of 10 X PCR buffer, 8 ml of DNTP,10 pM of each nucleic acid primer and 1 U Taq Polymerase. 10 ml of DNA template added to make up the volume to 50 ml. PCR amplification condition of each cycle included: denaturation, primer annealing and primer extension polymerization. An initial denaturation at 95°C for 5 mins to obtain adequate denaturation of template DNA was also included in the programme. After 35 cycles an additional extension step was programmed at 72°C for 10 min in thermal cycler. PCR products analyzed by gel electrophoresis, the fungal product showed 601bp band after amplification.