Amoebidium species are single-celled, cigar-shaped or tubular in vegetative growth form (= thallus), and attach to the exoskeleton of various freshwater arthropod hosts (Crustaecea or Insecta) by means of a secreted, glue-like basal holdfast.

[9] The classification of Amoebidium and Paramoebidium with the fungal trichomycetes was early considered tenuous due to the production of amoeboid dispersal cells,[12][13] a feature not seen among Fungi.

[11][14] However, their overall morphology (i.e. hair-like growth form with a basal holdfast), production of spores, and residence in the digestive tract of arthropods were considered strong enough characters to include them with the fungal trichomycetes until additional evidence could resolve their placement.

[4] The analyses of Cafaro[3] showed a monophyletic relationship between Amoebidium and Paramoebidium, although his dataset had limited taxon sampling with one representative sequence from each genus.

However, a recent molecular phylogenetic analysis of the Ichthyophonida that included broad taxon and gene sampling found evidence of polyphyly between Amoebidium and Paramoebidium.