Microbial mats are benthic communities of a variety of microorganisms. Their investigation requires multidisciplinary studies and close cooperation between microbiologists, biogeochemists, and geologists. Reported here are recent advances in the study of structure, development and ecological relationships. The methodology described includes microsensors as well as new molecular techniques for the detection and identification of microorganisms. Increasing interest exists for applied aspects, e.g. the possibility to use natural or constructed microbial mats for the degradation of xenobiotics, for site remediation, etc.