Autogamy or self-fertilization refers to the fusion of two gametes that come from one individual. Autogamy is predominantly observed in the form of self-pollination, a reproductive mechanism employed by many flowering plants. However, species of protists have also been observed using autogamy as a means of reproduction. Flowering plants engage in autogamy regularly, while the protists that engage in autogamy only do so in stressful environments.

Paramecium aurelia is the most commonly studied protozoan for autogamy. Similar to other unicellular organisms, Paramecium aurelia typically reproduce asexually via binary fission or sexually via cross-fertilization. However, studies have shown that when put under nutritional stress, Paramecium aurelia will undergo meiosis and subsequent fusion of gametic-like nuclei. This process, defined as hemixis, a chromosomal rearrangement process, takes place in a number of steps. First, the two micronuclei of P. aurelia enlarge and divide two times to form eight nuclei. Some of these daughter nuclei will continue to divide to create potential future gametic nuclei. Of these potential gametic nuclei, one will divide two more times. Of the four daughter nuclei arising from this step, two of them become anlagen, or cells that will form part of the new organism. The other two daughter nuclei become the gametic micronuclei that will undergo autogamous self-fertilization. These nuclear divisions are observed mainly when the P. aurelia is put under nutritional stress. Research shows that P. aurelia undergo autogamy synchronously with other individuals of the same species.

In Paramecium tetraurelia, vitality declines over the course of successive asexual cell divisions by binary fission. Clonal aging is associated with a dramatic increase in DNA damage. When paramecia that have experienced clonal aging undergo meiosis, either during conjugation or automixis, the old macronucleus disintegrates and a new macronucleus is formed by replication of the micronuclear DNA that had just experienced meiosis followed by syngamy. These paramecia are rejuvenated in the sense of having a restored clonal lifespan. Thus it appears that clonal aging is due in large part to the progressive accumulation of DNA damage, and that rejuvenation is due to repair of DNA damage during meiosis that occurs in the micronucleus during conjugation or automixis and reestablishment of the macronucleus by replication of the newly repaired micronuclear DNA.

Similar to Paramecium aurelia, the parasitic ciliate Tetrahymena rostrata has also been shown to engage in meiosis, autogamy and development of new macronuclei when placed under nutritional stress. Due to the degeneration and remodeling of genetic information that occurs in autogamy, genetic variability arises and possibly increases an offspring's chances of survival in stressful environments.

Allogromia laticollaris is perhaps the best-studied foraminiferan amoeboid for autogamy. A. laticollaris can alternate between sexual reproduction via cross-fertilization and asexual reproduction via binary fission. The details of the life cycle of A. laticollaris are unknown, but similar to Paramecium aurelia, A. laticollaris is also shown to sometimes defer to autogamous behavior when placed in nutritional stress. As seen in Paramecium, there is some nuclear dimorphism observed in A. laticollaris. There are often observations of macronuclei and chromosomal fragments coexisting in A. laticollaris. This is indicative of nuclear and chromosomal degeneration, a process similar to the subdivisions observed in P. aurelia. Multiple generations of haploid A. laticollaris individuals can exist before autogamy actually takes place. The autogamous behavior in A. laticollaris has the added consequence of giving rise to daughter cells that are substantially smaller than those rising from binary fission. It is hypothesized that this is a survival mechanism employed when the cell is in stressful environments, and thus not able to allocate all resources to creating offspring. If a cell was under nutritional stress and not able to function regularly, there would be a strong possibility of its offspring's fitness being sub-par.

About 10–15% of flowering plants are predominantly self-fertilizing. Self-pollination is an example of autogamy that occurs in flowering plants. Self-pollination occurs when the sperm in the pollen from the stamen of a plant goes to the carpels of that same plant and fertilizes the egg cell present. Self-pollination can either be done completely autogamously or geitonogamously. In the former, the egg and sperm cells that unite come from the same flower. In the latter, the sperm and egg cells can come from a different flower on the same plant. While the latter method does blur the lines between autogamous self-fertilization and normal sexual reproduction, it is still considered autogamous self-fertilization.

Self-pollination can lead to inbreeding depression due to expression of deleterious recessive mutations. Meiosis followed by self-pollination results in little genetic variation, raising the question of how meiosis in self-pollinating plants is adaptively maintained over an extended period in preference to a less complicated and less costly asexual ameiotic process for producing progeny. For instance, Arabidopsis thaliana is a predominantly self-pollinating plant that has an outcrossing rate in the wild estimated at less than 0.3%, and self-pollination appears to have evolved roughly a million years ago or more. An adaptive benefit of meiosis that may explain its long-term maintenance in self-pollinating plants is efficient recombinational repair of DNA damage.

There are basically two distinct types of sexual reproduction among fungi. The first is outcrossing (in heterothallic fungi). In this case, mating occurs between two different haploid individuals to form a diploid zygote, that can then undergo meiosis. The second type is self-fertilization or selfing (in homothallic fungi). In this case, two haploid nuclei derived from the same individual fuse to form a zygote than can then undergo meiosis. Examples of homothallic fungi that undergo selfing include species with an aspergillus-like asexual stage (anamorphs) occurring in many different genera, several species of the ascomycete genus Cochliobolus, and the ascomycete Pneumocystis jirovecii (for other examples, see Homothallism). A review of evidence on the evolution of sexual reproduction in the fungi led to the concept that the original mode of sexual reproduction in the last eukaryotic common ancestor was homothallic or self-fertile unisexual reproduction.