Pebrine is one of the devastating diseases mostly caused by notorious Nosema - a microsporidian infecting silkworms. Identification of novel genes associated with the pathogen plays a key role in developing a reliable diagnostic tool for the detection of disease. Targeting potential biomarkers will help in developing strategies for fast and efficient control measures, which can prevent the spread of infection. This study was to identify genes present commonly in Nosema such as Nosema bombycis, Nosema mylitta, Nosema assamensis and Nosema ricini infecting Indian silkworms in order to find potential gene markers for early pebrine disease diagnosis. Real time PCR was used to validate the genes active early during the infection cycle, confirming the expression of genes and their order of expression. 16S rRNA and β-tubulin were found to be expressed early in infection followed by PTP1 and PTP2, PTP3, SWP5 and MetAP2 genes. These identified molecular markers can be used in addition to conventional gene primers which are traditionally used for the detection of pebrine.