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Pollution caused by heavy metals is a serious threat for the environment and human health, because of their toxicity and persistency. Among heavy metals, arsenic represents a harsh pollutant able to contaminate air, water and soil; it is a component of the Earth crust and is present in many geothermal environments, but it is also released into the environment by the consumption of arsenic-containing products such as insecticides, pesticides, and chemotherapeutic drugs. Most of the current systems for monitoring and restoring the environment from heavy metals require several expensive and hard instrumentation; modern biotechnologies can be addressed to exploit metal bio-transformations for the set-up of easier and possibly cheaper devices and eco-sustainable processes. In this context thermophiles stand out, they are microorganisms adapted to live in harsh conditions, which often include high concentrations of heavy metals. Therefore, knowledges of their resistance mechanisms can lead to the development of new strategies to face the heavy metals pollution. Moreover, thermophilic microorganisms have been associated to sources of thermostable proteins and enzymes useful for several applications; in fact, since the last 30 years they have been deeply studied for their high potential in industrial biotechnologies. This PhD thesis is aimed at the exploitation of thermophilic microorganisms for environmental applications. In particular we here report the state of the art on the most common thermophilic resistance mechanisms to heavy metals (Chapter [2]); we also describe the set-up of electrochemical and optical biosensors for the monitoring of arsenic based on thermophilic enzymes (Chapter [3]), as well as the isolation and physiological, molecular and genetic characterization of new metal-tolerant thermophiles from extreme environments (Chapter [4]) as source of novel biomolecules and/or bioprocesses. Furthermore, we report the emerging technologies for genetic engineering of thermophilic microorganisms, and their employment against, not only heavy metals, but also organic pollutants and in the lignocellulose degradation (Chapter [5]).