Saudi Aramco has an interest to monitor crude oil pipelines for the presence of microbially influenced corrosion (MIC) and to identify the potential for MIC in individual pipelines. In order to perform such a monitoring in a thorough and cost-efficient manner laboratory kits and protocols for detection and enumeration of MIC-related microorganisms by Molecular Microbiology Methods (MMM) must be customized for the crude oil pipelines system. This paper discusses the research being conducted in Saudi Aramco (SA) Research and Development Center (R&DC) and the Danish Technology Institute (DTI) to (i) develop protocols for cell- and DNA extraction from Saudi Arabian crude oil samples (ii) compare the microbial community structure in samples of crude and water from crude oil pipelines and (iii) design MMM assays suitable for surveillance and troubleshooting related to MIC in crude oil pipelines. Together these activities outline a roadmap for the implementation of MMM-based MIC surveillance in crude and water pipelines as well as other industrial installations. It is expected that the investment necessary for this implementation will be returned manifold through early-warning and a more focused and efficient mitigation of MIC.