Speciation is the process by which new species form. It begins with the isolation of two populations. If two populations are to become sufficiently distinct that interbreeding is difficult or impossible, then there must be relatively little gene flow (migration) between them (because if there were a great deal of gene flow, then genetic changes in one population would soon become widespread in the other as well). However, it is not enough for the two populations to simply be isolated; they will become separate species only if, during the period of isolation, they evolve sufficiently large genetic differences. Thus the second factor in species formation is genetic divergence. The genetic differences must be large enough that if the isolated populations are reunited, they can no longer interbreed and produce vigorous, fertile offspring. If isolated populations are small, chance events may generate significant genetic differences by genetic drift (changes in the frequency of a characteristic in a population caused by chance rather than reproductive fitness). In both small and large populations, different environmental pressures in separate environments may favor the evolution of large genetic differences.

Speciation has seldom been observed in the wild. Nevertheless, evolutionary biologists have synthesized theories, observations, and experiments to devise hypothetical mechanisms for the origin of new species. These mechanisms fall into two broad categories: (1) allopatric speciation, in which two populations are geographically separated from one another, and (2) sympatric speciation, in which two populations share the same geographical area.

At first glance, it might seem that sympatric speciation violates the principle of isolation of populations, because the speciating populations live in the same locale. However, it is isolation from gene flow that is crucial to speciation. Although such isolation may be most commonly imposed by a physical barrier such as a river, two populations living in the same area can also experience restricted gene flow if they occupy different habitats within the area (for example, marshes as opposed to forests) or breed in different non-overlapping time periods. Therefore, the principle still holds: isolation from gene flow is the key to both allopatric and sympatric speciation.

Allopatric speciation can occur when different parts of a population become physically separated by a difficult-to-cross barrier. Physical separation could occur, for example, if some members of a population of land-dwelling organisms drifted, swam, or flew to a remote oceanic island. A population of water-dwelling organisms might be split when geological processes such as volcanism or continental drift create new land barriers that subdivide previously continuous seas or lakes. Geological change can also divide terrestrial populations. Portions of populations can become stranded in patches of suitable habitat that become isolated by climate shifts.

If two or more populations become geographically isolated for any reason, little or no migration (and therefore little or no gene flow) can occur between them. If the pressures of natural selection differ in the separate locations, then the populations may accumulate genetic differences. Genetic differences may also arise if one or more of the separated populations is small enough for genetic drift to occur. For example, genetic drift may be especially likely in the aftermath of a founder event, in which a few individuals become isolated from the main body of the species. In either case, genetic differences between the separated populations may eventually become large enough to make interbreeding impossible. At that point, the two populations will have become separate species. Most biologists believe that geographic isolation followed by allopatric speciation has been the most common source of new species, especially among animals.

Sympatric speciation occurs within a single geographic area. Like allopatric speciation, it requires limited gene flow. One of the likely mechanisms whereby gene flow can be reduced between members of a single population in a given area is ecological isolation. If the same geographical area contains two distinct types of habitats (for example, distinct food sources, nesting places, and so on), different members of a single species may begin to specialize in one habitat or the other. If conditions are right, natural selection for habitat specialization may cause the formerly single species to split into two species.