Mastigamoeba is a genus of pelobionts, and treated by some as members of the Archamoebae group of protists. Mastigamoeba are characterized as anaerobic, amitochondriate organisms that are polymorphic. Their dominant life cycle stage is as an amoeboid flagellate. Species are typically free living, though endobiotic species have been described.

The genus is relatively understudied, and under contention regarding the composition of the genus. While dozens of species have been described (some in other genera such as Phreatamoeba, Dinamoeba, and Mastigina), the well described species are Mastigamoeba aspera Schulze, 1875; Mastigamoeba simplex Kent, 1880; Mastigamoeba chlamys Frenzel, 1897 Lemmermann, 1914; Mastigamoeba viridis Prowazek, 1900; Mastigamoeba trichophora Lauterborn, 1901; Mastigamoeba balamuthi (Chàvez et al., 1986) Simpson et al., 1997; Mastigamoeba schizophrenia Simpson et al., 1997; and Mastigamoeba punctachora Bernard, Simpson and Patterson, 2000. Mastigamoeba balamuthi was initially referred to as Phreatamobea balamuthi and are treated by some as indistinguishable at the generic level, though this is not universally accepted. All species share many similarities with other pelobionts, such as Mastigella and the related Entamoeba.

It includes Mastigamoeba balamuthi.

A strain previously called as Mastigamoeba invertens (ATCC 50338) is now classified as Breviata anathema.

Mastigamoeba was described as a genus of species characterized by an ameboid body with a hyaline based cytoplasm and a flagellum. Due to its similarities to genera such as Mastigella and Mastigina, the genus Mastigamoeba was specified in 1891 to only include organisms with the following features: amoeboid flagellates with hyaline based cytoplasm, a direct connection between the flagellum and the nucleus, on occasions with lateral pseudopods, and nucleus with an elongated shape. Throughout the 20th century, hundreds of species were described under the genus Mastigamoeba based on external morphological characteristics alone. However, recent discoveries regarding life cycles have shown that a single organism takes on many morphologies throughout its life cycle, putting the number of described species into question. There are currently nine confirmed distinguished species of Mastigamoeba, with many more in contention. Tom Cavalier-Smith described the class Archamoebae in 1983 and among others included the order Mastigamoebid, which includes the genus Mastigamoeba. 

Historically, amoeboid flagellates have been considered Pelobionts, which encompasses mastigamoebids and pelomyxids.

Mastigamoebae are a type of pelobiont. Pelobionts are considered microoxic; they thrive in environments with 10-20% of atmospheric oxygen such as in upper mud or sand layers, or the water-sediment surface of shallow ponds. Some have been found in sewage treatment plants. Pelobionts are typically found worldwide, with studies confirming their extensive presence in temperate regions of Europe and North America. Habitats typically include freshwater rivers and lakes, with the highest abundance of organisms in stagnant water, where low-oxygen environments are common. Marine environments are also found to host pelobionts. Habitats in which pelobionts are found are organically rich.

Though most pelobionts are free-living, some members are considered endobiotic, meaning they survive only in the guts of hosts. These members are completely anoxic, and thrive in areas of low pH. They have been found in various vertebrate and invertebrate hosts, particularly within primates and dogs.