Chemical ecology is a vast and interdisciplinary field utilizing biochemistry, biology, ecology, and organic chemistry for explaining observed interactions of living things and their environment through chemical compounds (e.g. ecosystem resilience and biodiversity). Early examples of the field trace back to experiments with the same plant genus in different environments, interaction of plants and butterflies, and the behavioral effect of catnip. Chemical ecologists seek to identify the specific molecules (i.e. semiochemicals) that function as signals mediating community or ecosystem processes and to understand the evolution of these signals. The chemicals behind such roles are typically small, readily-diffusible organic molecules that act over various distances that are dependent on the environment (i.e. terrestrial or aquatic) but can also include larger molecules and small peptides.

In practice, chemical ecology relies on chromatographic techniques, such as thin-layer chromatography, high performance liquid chromatography, gas chromatography, mass spectrometry (MS), and absolute configuration utilizing nuclear magnetic resonance (NMR) to isolate and identify bioactive metabolites. To identify molecules with the sought-after activity, chemical ecologists often make use of bioassay-guided fractionation. Today, chemical ecologists also incorporate genetic and genomic techniques to understand the biosynthetic and signal transduction pathways underlying chemically mediated interactions.

Plant, microbe, and insect chemical ecology focuses on the role of chemical cues and signals in mediating interactions with their abiotic (e.g. ability of some bacterium to reduce metals in the surrounding environment) and biotic environment (e.g. microorganisms, phytophagous insects, and pollinators). Cues allow for organisms to monitor interactions with the environment and to adjust accordingly through changes in chemical abundance as a response. Changes in compound abundance allows for defensive measures to be enacted, e.g. attracts for predators.

The chemical ecology of plant-insect interaction is a significant subfield of chemical ecology. In particular, plants and insects are often involved in a chemical evolutionary arms race. As plants develop chemical defenses to herbivory, insects which feed on them co-evolved to develop immunity to these poisons, and in some cases, repurpose these poisons for their own chemical defense against predators. For example, caterpillars of the monarch butterfly sequester cardenolide toxins from their milkweed host-plants and are able to use them as an anti-predator defense due to the toxin. Sequestering is a strategy of the co-evolution, feeding experiments on caterpillars of the monarch butterfly showed caterpillars which have not feed on milkweed do not pose similar toxins as those found to feed on milkweed. Whereas most insects are killed by cardenolides, which are potent inhibitors of the Na+/K+-ATPase, monarchs have evolved resistance to the toxin over their long evolutionary history with milkweeds. Other examples of sequestration include the tobacco hornworm Manduca sexta, which use nicotine sequestered from tobacco plants in predator defense; and the bella moth, which secretes a quinone-containing froth to deter predators obtained from feeding on Crotalaria plants as a caterpillar.

Chemical ecologists also study chemical interactions involved in indirect defenses of plants, such as the attraction of predators and parasitoids through herbivore-induced volatile organic compounds (VOCs).

Plant interactions with microorganisms are also mediated by chemistry. Both constitutive and induced secondary metabolites (specialized metabolites in modern terminology) are involved in plant defense against pathogens and chemical signals are also important in the establishment and maintenance of resource mutualisms. For example, both rhizobia and mycorrhizae depend on chemical signals, such as strigolactones and flavanoids exuded from plant roots, in order to find a suitable host.

For microbes to gain access to the plant, they must be able to penetrate the layer of wax that forms a hydrophobic barrier on the plant's surface. Many plant-pathogenic microbes secrete enzymes that break down these cuticular waxes. Mutualistic microbes on the other hand may be granted access. For example, rhizobia secrete Nod factors that trigger the formation of an infection thread in receptive plants. The rhizobial symbionts can then travel through this infection thread to gain entrance to root cells.

Mycorrhizae and other fungal endophytes may also benefit their host plants by producing antibiotics or other secondary metabolites/ specialized metabolites that ward off harmful fungi, bacteria and herbivores in the soil. Some entomopathogenic fungi can also form endophytic relationships with plants and may even transfer nitrogen directly to plants from insects they consume in the surrounding soil.