If organism identification is needed the analysis of DNA fingerprints is method of choice.
For identification so called DNA barcoding method can be used. This method uses a DNA analysis of specific sequences to identify an unknown sample in terms and classify it to particular species.
The most commonly used barcode region for animals is a segment of the mitochondrial gene cytochrome oxidase I (COX), for fungi the more specific sequence is Internal Transcribed Spacer 2 (ITS2) between rRNA genes is used.
For microorganism detection the 16S rRNA gene is the best, because is enough species specific and easily to analyse.
Applications include, for example, products in commerce (herbal supplements, wood, or skins and other animal parts, contamination in protein production, etc.).