Microbiologically influenced corrosion (MIC) has been determined to be the leading cause of corrosion in pipelines and equipment in a crude oil processing facility. A high number of corrosion- causing microorganisms have been detected in the on-the-plot pipes and facilities, crude oil flow lines and trunk lines. To determine the source of corrosive microorganisms in crude transportation pipelines and processing facilities, production water samples, injection seawater samples, and downhole samples were analyzed using conventional most probable number (MPN) method to enumerate viable general heterotrophic bacteria (v-GHB) and sulfate-reducing bacteria (v-SRB), spore-forming GHB (s-GHB), and spore-forming SRB (s-SRB). In addition, gene-based quantitative polymerase chain reaction (qPCR) analysis was used to detect and quantify general bacteria, mesophilic SRB (m-SRB), s-SRB, thermophilic SRB (t-SRB), and sulfate-reducing archaea (SRA). The analyses revealed the presence of high number of general bacteria populations, including spore-forming GHB, in injection seawater and production water, and moderate number of general bacteria in downhole samples. Moderate levels of m-SRB and s-SRB were found, respectively, in injection water and downhole samples. s-SRB, t-SRB, and SRA were also detected in all injection seawater and production water samples. The presence of high load of microorganisms in the injection seawater introduces the exogenous microbes into reservoir and may pose a risk to the reservoir souring and plugging. In addition, the presence of a high number of microorganisms in production water poses a risk to contaminate transportation pipelines and crude processing facilities and result in corrosion. It is concluded that microorganisms colonizing the flow lines, trunk lines, and other downstream facilities can potentially be traced back to the microbes in the producer crude oil, to the reservoir, and finally to the injected seawater. An effective MIC management program should include a proper microbial monitoring program, and an effective treatment program, to ensure injection water quality, and if necessary, include a treatment program on crude streams to control microbial activity during transportation and processing.