Metagenomics is the genomic analysis of the collective genomes of an assemblage of organisms, or the metagenome. Metagenomic analysis has been applied to diverse problems in microbiology and has yielded insight into the physiology of uncultured organisms to access the potentially useful enzymes and secondary metabolites they produce. DNA isolation methods have to be strictly adapted to the type of isolated biological material; of great importance is also the size of the obtained DNA. Small DNA fragments are usually sufficient for an analysis of individual genes or their small groups, whereas large inserts are required for analysing metabolic pathways, genome structures or sequencing large DNA fragments. There are two types of methods of extracting genomic DNA. One of them consists of the direct extraction of nucleic acids from an environmental sample after the cell lysis (in situ), followed by purification of the obtained DNA. The other method consists of the separation of bacterial cells from an environmental sample, followed by lysis of the cell suspension and DNA extraction. In the presented review methods of the environmental DNA isolation, cloning and new enzymes discovery are presented.