Photosynthetic microbial mats are metabolically structured systems driven by solar light. They are ubiquitous and can grow in hydrocarbon-polluted sites, Our aim is to determine the impact of chronic hydrocarbon contamination on the structure, activity, and functioning of a microbial mat. We compared it to an uncontaminated mat harboring similar geochemical characteristics. The mats were sampled in spring and fall for 2 years. Seasonal variations were observed for the reference mat: sulfur cycle-related bacteria dominated spring samples, while Cyanobacteria dominated in autumn. The contaminated mat showed minor seasonal variation; a progressive increase of Cyanobacteria was noticed, indicating a perturbation of the classical seasonal behavior. Hydrocarbon content was the main factor explaining the differences in the microbial community structure; however, hydrocarbonoclastic bacteria were among rare or transient Operational Taxonomic Units (OTUs) in the contaminated mat We suggest that in long-term contaminated systems, hydrocarbonoclastic bacteria cannot be considered a sentinel of contamination.