Microbial mats from Salins-de-Giraud (Camargue, France) and Guérande (Bretagne, France) were maintained in microcosm to determine the impact of crude oil contamination on bacterial communities. Terminal Restriction Fragment Length Polymorphism (T-RFLP) analyses revealed noticeable changes in the bacterial community structures concomitant with petroleum degradation. The results demonstrate clearly different periods with a succession of different bacterial populations. Operational Taxonomic Units (OTUs) that could be related to Chloroflexus, Burkholderia, Desulfovibrio and Cytophaga genera were found among the populations well adapted to crude oil exposure. To further evaluate the metabolic ability to degrade hydrocarbons of such oil contaminated microbial communities, we studied the diversity of the genes encoding enzymes known to be involved in hydrocarbon compounds degradation: the naphthalene and the phenanthrene dioxygenases. This analyses indicated that although diverse Polyciclic Aromatic Hydrocarbons (PAH) dioxygenases encoding genes were detected after a three months period of contamination, they were mainly represented by only three different types. Thus, taxonomic (16S rRNA encoding gene) and functional (dioxygenases encoding gene) diversity analysis indicated that microbial communities of microbial mats may adapt to oil pollution. Therefore, such bacterial ecosystems could play a key role in hydrocarbon degradation in coastal zones.