The Botanical and Zoological Codes of nomenclature treat the concept of synonymy differently.

• In botanical nomenclature, a synonym is a scientific name that applies to a taxon that (now) goes by a different scientific name. For example, Linnaeus was the first to give a scientific name (under the currently used system of scientific nomenclature) to the Norway spruce, which he called Pinus abies. This name is no longer in use, so it is now a synonym of the current scientific name, Picea abies.
• In zoology, moving a species from one genus to another results in a different binomen, but the name is considered an alternative combination rather than a synonym. The concept of synonymy in zoology is reserved for two names at the same rank that refers to a taxon at that rank – for example, the name Papilio prorsa Linnaeus, 1758 is a junior synonym of Papilio levana Linnaeus, 1758, being names for different seasonal forms of the species now referred to as Araschnia levana (Linnaeus, 1758), the map butterfly. However, Araschnia levana is not a synonym of Papilio levana in the taxonomic sense employed by the Zoological code.

Unlike synonyms in other contexts, in taxonomy a synonym is not interchangeable with the name of which it is a synonym. In taxonomy, synonyms are not equals, but have a different status. For any taxon with a particular circumscription, position, and rank, only one scientific name is considered to be the correct one at any given time (this correct name is to be determined by applying the relevant code of nomenclature). A synonym cannot exist in isolation: it is always an alternative to a different scientific name. Given that the correct name of a taxon depends on the taxonomic viewpoint used (resulting in a particular circumscription, position and rank) a name that is one taxonomist's synonym may be another taxonomist's correct name (and vice versa).

Synonyms may arise whenever the same taxon is described and named more than once, independently. They may also arise when existing taxa are changed, as when two taxa are joined to become one, a species is moved to a different genus, a variety is moved to a different species, etc. Synonyms also come about when the codes of nomenclature change, so that older names are no longer acceptable; for example, Erica herbacea L. has been rejected in favour of Erica carnea L. and is thus its synonym.