Amoebidium is a genus of small protists that form walled, hairlike microthalli on the external surface of freshwater crustacea and insect larvae, including mosquitos. The genus name, which means "little amoeba", refers to the amoeboid cells that the thalli may produce during asexual reproduction. The four described species are probably distributed worldwide, but because of their small size and unusual habit, they are not often seen or recorded. The related genus Paramoebidium, with seven described species, differs from Amoebidium primarily in habitat, which is in the hindgut of aquatic insect larvae and crustaceans. These protists appear to be passengers, not parasites; the host animals do not appear to be affected by their presence.

Organisms that have the same microthallus shape as Amoebidium, and occur in similar habitats, have been called trichomycetes. Most trichomycetes are, in fact, fungi, as the name indicates, but Amoebidium and Paramoebidium are not. Instead, they are among the several groups of protists, including choanoflagellates, ichthyosporeans = mesomycetozoans, and nucleariid amoebae, that belong to the same lineage as animals and fungi. The mitochondrial genome of A. parasiticum has one of the most complex and unusual organizations known in nature.