Fungi are a diverse group of organisms that employ a huge variety of reproductive strategies, ranging from fully asexual to almost exclusively sexual species. Most species can reproduce both sexually and asexually, alternating between haploid and diploid forms. This contrasts with most multicellular eukaryotes, such as mammals, where the adults are usually diploid and produce haploid gametes which combine to form the next generation. In fungi, both haploid and diploid forms can reproduce – haploid individuals can undergo asexual reproduction while diploid forms can produce gametes that combine to give rise to the next generation.

Mating in fungi is a complex process governed by mating types. Research on fungal mating has focused on several model species with different behaviour. Not all fungi reproduce sexually and many that do are isogamous; thus, for many members of the fungal kingdom, the terms "male" and "female" do not apply. Homothallic species are able to mate with themselves, while in heterothallic species only isolates of opposite mating types can mate.

Mating between isogamous fungi may consist only of a transfer of a nucleus from one cell to another. Vegetative incompatibility within species often prevents a fungal isolate from mating with another isolate. Isolates of the same incompatibility group do not mate or mating does not lead to successful offspring. High variation has been reported including same-chemotype mating, sporophyte to gametophyte mating and biparental transfer of mitochondria.

A zygomycete hypha grows towards a compatible mate and they both form a bridge, called a progametangia, by joining at the hyphal tips via plasmogamy. A pair of septa forms around the merged tips, enclosing nuclei from both isolates. A second pair of septa forms two adjacent cells, one on each side. These adjacent cells, called suspensors provide structural support. The central cell, called the zygosporangium, is destined to become a spore. The zygosporangium is a unique structure to the Zygomycota and is easily recognizable in microscopy due to its characteristic dark color and spiky shape. The nuclei join in a process called karyogamy to form a zygote, which grows into a mature diploid zygomycete. A diploid zygomycete can then undergo meiosis to create spores, which disperse and germinate. The following generations of mycelium can undergo asexual or sexual reproduction.

The phylum Zygomycota has since been split into two phyla believed to be monophyletic, Mucoromycota and Zoopagomycota (later raised to the subkingdom rank as Mucoromyceta and Zoopagomyceta). Nevertheless, the two subkingdoms still conform to the behavior described above: "sexual reproduction, if present, via zygospores by gametangial conjugation".

As it approaches a mate, a haploid sac fungus develops one of two complementary organs, a "female" ascogonium or a "male" antheridium. These organs resemble gametangia except that they contain only nuclei. A bridge, the trichogyne forms, that provides a passage for nuclei to travel from the antheridium to the ascogonium. A dikaryon grows from the ascogonium, and karyogamy occurs in the fruiting body.

Neurospora crassa is a type of red bread mold of the phylum Ascomycota. N. crassa is used as a model organism because it is easy to grow and has a haploid life cycle: this makes genetic analysis simple, since recessive traits will show up in the offspring. Analysis of genetic recombination is facilitated by the ordered arrangement of the products of meiosis within a sac-like structure called an ascus (pl. asci). In its natural environment, N. crassa lives mainly in tropical and sub-tropical regions. It often can be found growing on dead plant matter after fires.

Neurospora was used by Edward Tatum and George Wells Beadle in the experiments for which they won the Nobel Prize in Physiology or Medicine in 1958. The results of these experiments led directly to the "one gene, one enzyme" hypothesis that specific genes code for specific proteins. This concept launched molecular biology. Sexual fruiting bodies (perithecia) can only be formed when two cells of different mating type come together (see Figure). Like other Ascomycetes, N. crassa has two mating types that, in this case, are symbolized by A and a. There is no evident morphological difference between the A and a mating type strains. Both can form abundant protoperithecia, the female reproductive structure (see Figure). Protoperithecia are formed most readily in the laboratory when growth occurs on solid (agar) synthetic medium with a relatively low source of nitrogen. Nitrogen starvation appears to be necessary for expression of genes involved in sexual development. The protoperithecium consists of an ascogonium, a coiled multicellular hypha that is enclosed in a knot-like aggregation of hyphae. A branched system of slender hyphae, called the trichogyne, extends from the tip of the ascogonium projecting beyond the sheathing hyphae into the air. The sexual cycle is initiated (i.e. fertilization occurs) when a cell, usually a conidium, of opposite mating type contacts a part of the trichogyne (see Figure). Such contact can be followed by cell fusion leading to one or more nuclei from the fertilizing cell migrating down the trichogyne into the ascogonium. Since both A and a strains have the same sexual structures, neither strain can be regarded as exclusively male or female. However, as a recipient, the protoperithecium of both the A and a strains can be thought of as the female structure, and the fertilizing conidium can be thought of as the male participant.