Abstract: The present study investigated the identities of endophytic bacteria isolated from the seeds of dry fruits of Capsicum chinensis Bhut Jolokia using PCR analysis with the view of food products quality. The bacteria were isolated from the seeds soaked in peptone broth followed by serial dilution. Standard molecular methods were used for DNA extraction (UniFlexTM DNA Isolation kit method), Polymerase Chain Reaction (PCR), Amplification, Electrophoresis, Purification and Sequencing of generated PCR products. The partial sequences obtained were deposited in the database of National Centre for Biotechnology Information (NCBI). Based on genotypic characteristics, these strains belonged to the genus Paenibacillus. Phylogenetic analysis based on 16S rRNA gene sequence comparison showed that they clustered with Paenibacillus illinoisensis (99 % similarity). It was assigned Paenibacillus illinoisensis strain Nagoth JAR 007 and was submitted to Genbank (KC886309). The research findings concluded that presence of the endophytic Paenibacillus are nonpathogenic and has a role in plant resistance to abiotic or biotic stress.