Protists are the eukaryotes that cannot be classified as plants, fungi or animals. They are mostly unicellular and microscopic. Many unicellular protists, particularly protozoans, are motile and can generate movement using flagella, cilia or pseudopods. Cells which use flagella for movement are usually referred to as flagellates, cells which use cilia are usually referred to as ciliates, and cells which use pseudopods are usually referred to as amoeba or amoeboids. Other protists are not motile, and consequently have no built-in movement mechanism.

Unicellular protists comprise a vast, diverse group of organisms that covers virtually all environments and habitats, displaying a menagerie of shapes and forms. Hundreds of species of the ciliate genus Paramecium  or flagellated Euglena  are found in marine, brackish, and freshwater reservoirs; the green algae Chlamydomonas is distributed in soil and fresh water world-wide; parasites from the genus Giardia colonize intestines of several vertebrate species. One of the shared features of these organisms is their motility, crucial for nutrient acquisition and avoidance of danger. In the process of evolution, single-celled organisms have developed in a variety of directions, and thus their rich morphology results in a large spectrum of swimming modes.

Many swimming protists actuate tail-like appendages called flagella or cilia in order to generate the required thrust. This is achieved by actively generating deformations along the flagellum, giving rise to a complex waveform. The flagellar axoneme itself is a bundle of nine pairs of microtubule doublets surrounding two central microtubules, termed the 9+2 axoneme, and cross-linking dynein motors, powered by ATP hydrolysis, perform mechanical work by promoting the relative sliding of filaments, resulting in bending deformations.

Although protist flagella have a diversity of forms and functions, two large families, flagellates and ciliates, can be distinguished by the shape and beating pattern of their flagella.

In the phylogenetic tree on the right, aquatic organisms (living in marine, brackish, or freshwater environments) have their branches drawn in blue while parasitic organisms have their branches drawn in red. Ciliates are indicated by an asterisk after their names. For each phylum marked in bold font, a representative organism has been sketched next to its name.

Flagella are used in prokaryotes (archaea and bacteria) as well as protists. In addition, both flagella and cilia are widely used in eukaryotic cells (plant and animal) apart from protists.

The regular beat patterns of eukaryotic cilia and flagella generates motion on a cellular level. Examples range from the propulsion of single cells such as the swimming of spermatozoa to the transport of fluid along a stationary layer of cells such as in a respiratory tract. Though eukaryotic flagella and motile cilia are ultrastructurally identical, the beating pattern of the two organelles can be different. In the case of flagella, the motion is often planar and wave-like, whereas the motile cilia often perform a more complicated three-dimensional motion with a power and recovery stroke.

Eukaryotic flagella—those of animal, plant, and protist cells—are complex cellular projections that lash back and forth. Eukaryotic flagella are classed along with eukaryotic motile cilia as undulipodia to emphasize their distinctive wavy appendage role in cellular function or motility. Primary cilia are immotile, and are not undulipodia.