In bacteria, conjugation is a method of gene transfer between individuals either by direct cell-to-cell contact or across a small gap called a 'mating bridge'. Like the similar processes of transformation and transduction, conjugation is a method of horizontal (or lateral) gene transfer; that is, the transfer of genetic information between individuals who are not parent and offspring.

The mechanism of conjugation usually involves the fertility (F) plasmid, although other plasmids and transposable elements may be exchanged by conjugation. Plasmids are circles of extra-chromosomal DNA which can offer both genetic advantages and disadvantages to their bacterial host, the advantages including antibiotic resistance, tolerance to environmental toxins and the ability to use new metabolites. It is by conjugation, then, that resistance to antibiotics can spread through a bacterial population.

The fertility plasmid is about 100kb long. Bacteria in possession of an F plasmid are known as F+ strains, while those without it are known as F- strains. Because the plasmid codes for its own transfer, these strains may also be known as donor and recipient strains, respectively. There can only be one copy of the F plasmid present in a bacterium at any one time.

The F plasmid has its own origin of replication, oriV, and origin of transfer, oriT. It also has tra and trb loci, which synthesise the sex pilus as well as various membrane proteins that link the F+ donor to the F- recipient. It is now believed that DNA is not passed directly down the pilus; this has been confirmed by experiments where conjugation has occurred even when the pilus is denatured. The pilus instead serves to recognise a recipient host and, in the case of F plasmids, it acts as a retractile motor, depolymerising its subunits from the cytoplasmic end of the donor individual in order to bring the recipient closer.

When conjugation is initiated by an environmental cue, an enzyme called relaxase (working either independently or with numerous other proteins in a complex called a relaxosome) creates a nick in the DNA at the origin of transfer, oriT of the conjugative plasmid. The nicked strand - or T strand - is separated from the unbroken strand and transferred to the recipient host in a 5'-to-3' direction. Nicking the DNA also leaves a free 3' OH group for rolling circle replication of the plasmid.

DNA replication then occurs in both bacteria involved, where in the donor the leading strand is synthesised and in the recipient the lagging strand is synthesised. On the completion of replication, the DNA strand is nicked at a nic site, and the two DNA molecules are separated, allowing the DNA in the recipient bacterium to circularise. The bacteria then separate, each containing a full copy of the conjugative plasmid.

Plasmid transfer is prevented between two F+ individuals because of surface exclusion molecules on their membranes which prevent recognition of the cell by a sex pilus.