Plasmids may be classified in a number of ways.  Plasmids can be broadly classified into conjugative plasmids and non-conjugative plasmids.  Conjugative plasmids contain a set of transfer genes which promote sexual conjugation between different cells. In the complex process of conjugation, plasmids may be transferred from one bacterium to another via sex pili encoded by some of the transfer genes (see figure). Non-conjugative plasmids are incapable of initiating conjugation, hence they can be transferred only with the assistance of conjugative plasmids.  An intermediate class of plasmids are mobilizable, and carry only a subset of the genes required for transfer. They can parasitize a conjugative plasmid, transferring at high frequency only in its presence.
Plasmids can also be classified into incompatibility groups.  A microbe can harbour different types of plasmids, but different plasmids can only exist in a single bacterial cell if they are compatible.  If two plasmids are not compatible, one or the other will be rapidly lost from the cell. Different plasmids may therefore be assigned to different incompatibility groups depending on whether they can coexist together.  Incompatible plasmids (belonging to the same incompatibility group) normally share the same replication or partition mechanisms and can thus not be kept together in a single cell.
Another way to classify plasmids is by function. There are five main classes:
* Fertility F-plasmids, which contain tra genes. They are capable of conjugation and result in the expression of sex pili.
* Resistance (R) plasmids, which contain genes that provide resistance against antibiotics or antibacterial agents. Historically known as R-factors, before the nature of plasmids was understood.
* Col plasmids, which contain genes that code for bacteriocins, proteins that can kill other bacteria.
* Degradative plasmids, which enable the digestion of unusual substances, e.g. toluene and salicylic acid.
* Virulence plasmids, which turn the bacterium into a pathogen. e.g. Ti plasmid in Agrobacterium tumefaciens
Plasmids can belong to more than one of these functional groups.