Low-level gene flow between species.

The idea of introgression predates that of horizontal gene transfer but nonetheless the two concepts are similar. Basically, both constitute the genetic migration of alleles between populations.

The major difference between the two is that introgression occurs particularly within the context of sexual reproduction, as that occurs with eukaryotes, whereas horizontal gene transfer occurs within the context of non-meiotic sexual processes, such as one sees with bacterial sex. In either case, a recombinant or hybrid organism is produced and the alleles associated with that organism either or do not survive.

With introgression that survival requires subsequent mating with one of the two (), i.e., subsequent, sexual, vertical gene transfer. With horizontal gene transfer as it occurs with mostly clonal organisms, that survival involves instead or subsequent asexual reproduction, which in principle should be easier to achieve.

In both of these cases, and despite the subtle differences, what is occurring is gene flow from one species into another species, which is then will be followed by a combination of genetic drift and natural selection, which together determine whether that gene flow is successful.

While speciation represents the separation of one gene pool into more than one gene pool, introgression represents basically a low-level incompleteness in that separation. See also allopolyploidy.