In this study the degradation of hydrophobic petroleum model compounds (phenanthrene, pristane, octadecane and dibenzothiophene) added to a submersed hypersaline microbial mat was investigated. Montmorillonite with an artificially altered, hydrophobic surface was used as carrier material, forming an organo-clay complex (OCC) with the attached mixture of petroleum model compounds. 6 mg/cm2 OCC were applied to cyanobacterial mat pieces, containing approximately 33.3 microg/mg OCC of each compound. The degradation experiment was performed under controlled laboratory conditions and accompanied by chemical analyses by GC/GC-MS, molecular analyses by PCR and DGGE as well as functional analyses by microsensor measurements of oxygen, photosynthesis, sulfide, pH and light. All applied model compounds were degraded, but residues were still present after 18 weeks. The aromatic compounds phenanthrene (5.1 microg/mg OCC) and dibenzothiophene (4.3 microg/mg OCC) were preferentially degraded compared to the alkanes pristane (12.4 microg/mg OCC) and n-octadecane (13.4 microg/mg OCC). Metabolic changes during the degradation process could not be detected by microsensor measurements. The molecular population analyses did not reveal any significant community changes concomitant with the decrease of the petroleum model compounds. We conclude, that the pristine mats represent an intact, robust ecosystem in which the enzymatic requirements for the degradation of the applied pollutants exist. The slow degradation process did not affect the usual high internal turnover rates and did not favor a certain population in the community of the mats.