Genome annotation is a process of identifying the locations of the genes and all of the coding regions in a genome and predicting the function of the proteins encoded by each gene. Kytococcus sedentarius is an aerobic, gram positive and opportunistic organism having callus degrading activity, associated with pitted keratolysis. K. sedentarius is of importance as it is the only known producer of the antibiotic monensin. The genome of K. sedentarius has already been annotated using the automated computer annotation programs; however, manual annotation is required because of potential inaccuracies in the computer annotation. The purpose of this study was to annotate the genes involved in short patch base excision repair in K. sedentarius. Base excision repair is among the most important mechanisms in all organisms as it prevents mutations in genes. The annotation was carried out using the Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT). Tools like BLAST, PSORT-B, TIGRFAM and KEGG were used to find the structure based similarity in orthologs, localization in the cell, structure and enzymatic activity respectively. The six genes annotated were found to be well conserved in K. sedentarius.