The present study aims at characterization of keratitis causing 56k protease encoding gene, and the homology modeling of this protease from Serratia marcescens. Keratitis is commonly caused by many bacteria such as Staphylococcus aureus, Pseudomonas aeruginosa, Serratia marcescens, viruses and fungi. The aim of the study is to isolate and culture Serratia marcescens, to identify it at the molecular level by amplifying its 16S rDNA and the 56k protease which is thought to be responsible for causing the disease. Both the 16S rDNA and the 56k protease gene were sequenced, and the same deposited in the GenBank with the accession numbers FJ588709 and FJ810078 respectively. The protein 56k protease was modelled and the protein was studied using bioinformatics approach.