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Microbiological surveys play a fundamental role in diagnosing and monitoring microbiologically influenced corrosion (MIC) threat in oil and gas systems. In the last decades, the microbiological characterization has been mostly carried out by the implementation of traditional growth-based techniques. However, with advances in biotechnology, molecular microbiological methods (MMMs), which are culture-independent techniques, have begun to replace the conventional methods. Currently, MMMs are being increasingly acknowledged as essential identification tools for MIC threat assessment. Diversity profile analysis based in next-generation sequencing (NGS) of the 16S rRNA gene is being used by the industry to help identify and characterize the total microbial community living in oil and gas production systems, which provides information to assess MIC risk or to predict possible MIC mechanisms. Even though MMMs have been included in the NACE standards, standardized protocols for collection, storage and preservation of oilfield samples have not been written. In this study, the effect of sample preservation on the results from 16S metagenomics analysis was investigated. Upon sample collection, microbial community structure presented significant changes as a result of the sample preservation conditions. Samples processed directly on-site showed higher diversity than samples transported to the laboratory for complete processing. Results of this research provide evidence of the importance of sample handling for an accurate microbial characterization and subsequent success in MIC prediction of oil and gas systems.