Bioprospecting (also known as biodiversity prospecting) is the exploration of natural sources for small molecules, macromolecules and biochemical and genetic information that could be developed into commercially valuable products for the agricultural, aquaculture, bioremediation, cosmetics, nanotechnology, or pharmaceutical industries. In the pharmaceutical industry, for example, almost one third of all small-molecule drugs approved by the U.S. Food and Drug Administration (FDA) between 1981 and 2014 were either natural products or compounds derived from natural products.

Terrestrial plants, fungi and actinobacteria have been the focus of many past bioprospecting programs, but interest is growing in less explored ecosystems (e.g. seas and oceans, caves and polar regions) and organisms (e.g. extremophiles, tropical corals and necrophages) as a means of identifying new molecules with novel biological activities. Species may be randomly screened for bioactivity or rationally selected and screened based on ecological, ethnobiological, ethnomedical, historical or genomic information.

When a region's biological resources or indigenous knowledge are unethically appropriated or commercially exploited without providing fair compensation, this is known as biopiracy. Various international treaties have been negotiated to provide countries legal recourse in the event of biopiracy and to offer commercial actors legal certainty for investment. These include the UN Convention on Biological Diversity and the Nagoya Protocol. The WIPO is currently negotiating more treaties to bridge gaps in this field.

Other risks associated with bioprospecting are the overharvesting of individual species and environmental damage, but legislation has been developed to combat these also. Examples include national laws such as the US Marine Mammal Protection Act and US Endangered Species Act, and international treaties such as the UN Convention on Biological Diversity, the UN Convention on the Law of the Sea, the Biodiversity Beyond National Jurisdictions Treaty, and the Antarctic Treaty.

Bioprospecting-derived resources and products used in agriculture include biofertilizers, biopesticides and veterinary antibiotics. Rhizobium is a genus of soil bacteria used as biofertilizers, Bacillus thuringiensis (also called Bt) and the annonins (obtained from seeds of the plant Annona squamosa) are examples of biopesticides, and valnemulin and tiamulin (discovered and developed from the basidiomycete fungi Omphalina mutila and Clitopilus passeckerianus) are examples of veterinary antibiotics.

Examples of bioprospecting products used in bioremediation include Coriolopsis gallica- and Phanerochaete chrysosporium-derived laccase enzymes, used for treating beer factory wastewater and for dechlorinating and decolorizing paper mill effluent.

Cosmetics and personal care products obtained from bioprospecting include Porphyridium cruentum-derived oligosaccharide and oligoelement blends used to treat erythema (rosacea, flushing and dark circles), Xanthobacter autotrophicus-derived zeaxanthin used for skin hydration and UV protection, Clostridium histolyticum-derived collagenases used for skin regeneration, and Microsporum-derived keratinases used for hair removal.

Because microbial laccases have a broad substrate range, they can be used in biosensor technology to detect a wide range of organic compounds. For example, laccase-containing electrodes are used to detect polyphenolic compounds in wine, and lignins and phenols in wastewater.