The MATBIOPOL project extensively studied the physical and biogeochemical characteristics as well as the related microbial processes and biodiversity in different mat systems. Not only did this information improve the understanding of microbial mat ecosystems, but also contributed to the assessment of the bioremediation potential of these microbial mats for oil-polluted sediments. Studies on the eco-important microorganisms in contaminated sediments provided interesting results on their biodiversity and physiology, and through chemical analyses on isolates, their capability to degrade selected hydrocarbons was evaluated. Researchers employed standard microbiology methodologies such as microscopic observations for morphology identification and biochemical methods including use of substrates, metabolism and specific optima in order to specify the related physiology. More specifically, most of the isolated heterotrophic hydrocarbon strains were characterised and specified as Pseudomonas spp., Acinetobacter spp. and Halomonas spp with the aid of conventionally used methods. Comparing results with molecular studies performed by other partners it was found that Marinobacter spp. display a wider geographic distribution in the microbial mats than it was initially thought. Screening studies on isolates showed that straight chain hydrocarbons could be widely used as substrates while degradation of mono-aromatic hydrocarbons could only be achieved on a certain extent. In particular, the Rhodococcus isolates showed increased potential of quickly degrading both individual hydrocarbons and specified hydrocarbon mixtures and thus may be used for cell bio-surfactants production.