Investigations on and applications of microorganisms in the agricultural activity and the environmental protection are increasing. Interest is mainly addressed to the selection of symbiont nitrogen-fixing and biofertilizing strains in order to increase the crop production and the biopesticide strain use; particularly Bacillus thuringiensis, his genes, which codify for the toxin synthesis, the specific DNA sequences of the different toxins are studied. In the field of the wastewater treatment, heavy metal removal, sludge anaerobic digestion and composting, unknown aspects of the processes are investigated and new potentialities of the microorganism applications are discovered. Considerable degradative capabilities of xenobiotic compounds are evidenced in many microbial strains; catabolic pathway and genetic determinants are studied. New microbial strains with expansion of metabilc activity and transgenic plants, obtained by cloning Bacillus thuringiensis genes, have been constructed. Advantages, limits and risks of genetic ingeenering and the importance of giving a new impulse also to the investigation on microbial biodiversity in the natural environment are discussed.