A symbiosis, derived from the Greek words "syn" (meaning with) and "biosis" (meaning living), is an intimate and often long-term association between members of different species. It is not necessarily mutualistic, i.e. beneficial to both partners, but can also be commensal (one species benefits, while the other is unaffected) or parasitic (one species benefits at a cost to the other). In a narrower sense, however, the term symbiosis refers to mutualistic relationships only. One partner can either live on (ectosymbiosis) or inside the other (endosymbiosis), and the association between them can either be essential for survival (obligate symbiosis) or not (facultative symbiosis).

Numerous animals rely on bacterial endosymbionts. Examples are shipworms (Teredo) and Xylophagus, which show wood-eating convergences to termites and some rodents (porcupine, beaver), the lucinid bivalves, which have evidently acquired symbiotic bacteria several times, and the vestimentiferans, deep-sea tubeworms that live in hydrothermal vents and cold seep areas. These worms have no functional gut and are entirely dependent on nutrients supplied by chemoautotrophic sulphur bacteria housed in so-called trophosomes in the worms' body cavity. Better known for their bacterial symbioses are insects such as sap-sucking aphids and psyllids, which have independently recruited different γ-proteobacteria (Buchnera and Carsonella) to provide them with essential amino acids. Aphids are involved in another fascinating mutualism that has evolved multiple times independently. As a result of their sugar-rich diet, aphids excrete vast quantities of honeydew, which is an important food source for many species of ants as well as a Madagascan gecko.

Insects are also famous for their symbioses with fungi, particularly attine ants (e.g. leaf-cutter ants), which tend fungal gardens and feed on the sugar-rich tips of the hyphae. Similar fungal cultivation has evolved at least twice in non-attine ants as well as in the termites and some beetles (notably ambrosia beetles). Interestingly, both leaf-cutter ants and ambrosia beetles carry bacterial symbionts that secrete antibiotics to prevent contamination of their fungal gardens with virulent fungal parasites.

In terms of associations, fungi are probably best known in lichens, where they form a symbiosis with a photosynthetic partner (either a cyanobacterium or a green alga and once a marine brown alga). Lichens provide prime examples of evolutionary convergence, as confirmed not only by the variety of partners and the precise nature of the symbiosis (some verge on parasitism), but also because different fungi have independently become lichen symbionts.

While many aspects of the origin of the eukaryotic cell are still very controversial, it is generally agreed that chloroplasts and mitochondria are the result of primary endosymbiosis, being derived from cyanobacteria and α-proteobacteria, respectively. In the case of chloroplasts there is some evidence that this endosymbiosis may have occurred more than once, and this view is supported by the ongoing symbiotic association between the amoeba Paulinella and a cyanobacterium that is not closely related to those that evolved into the chloroplasts. Not only are there intriguing parallels in the story of gene loss in chloroplasts and mitochondria, but we also find the re-invention of bacterial pathways, such as quinol oxidation.

Various marine animals such as foraminiferans, radiolarians, sea slugs and, most famously, corals have acquired endosymbiotic flagellate protozoans, the zooxanthellae. Most are autotroph and provide the host with energy in the form of photosynthetic products, in return for protection, nutrients and CO₂.

Amongst the numerous examples of plant-insect symbioses is the famous association between the yucca plant and its obligate pollinator, the yucca moth, which has evolved at least twice. Ants have repeatedly evolved multiple mutualistic relationships with so-called ant plants, which they protect from pests and competitors in exchange for shelter.