Microbiologically Influenced Corrosion (MIC) activities are mostly monitored by using canonical culture-based methods. However, these methods detect only culturable bacteria or require months of incubation to get results. To overcome this, molecular detection methods were developed for many of the MIC-causing microbes but were not available for Iron Reducing Bacteria (IRB) and Thiosulfate Reducing Bacteria (TRB). IRB and TRB are among the dominant group of microbes involved in corrosion and souring oil and gas infrastructures. In the present study, molecular probes were developed for IRB and TRB by targeting functional genes implicated in iron and thiosulfate reduction, respectively. Candidate gene sequences were retrieved from genome repository databases of pure isolates or metagenomic sequences. The sequences were aligned using bioinformatic software and primer-based probes were developed from conserved regions. Specificity and efficiency of the primers were validated by amplifying the sequences of target and non-target microbes using Quantitative Polymerase Chain Reaction (qPCR) methods. The probes successfully detected candidate microbes in biocorrosion samples collected from various gas processing facilities. The identified primer-based probes will help oil and gas industries to monitor MIC activities and develop timely management strategies to prevent undesirable microbial activities while improving system integrity and safety concerns.