Protozoa

Amoebae: pseudopodia
- Obligate parasites
  - Non-pathogenic
    - Entamoeba coli, Entamoeba dispar, Entamoeba hartmanii, and Entamoeba polecki
    - Endolimax nana
    - Iodamoeba buetschlii
  - Pathogenic
    - Entamoeba histolytica
    - Blastocystis hominis (maybe)
- Facultative free-living parasites
  - Naegleria fowleri: causes primary amoebic meningoencephalitis
  - Balamuthia mandrillaris: causes granulomatous amoebic encephalitis
  - Acanthamoeba species: cause granulomatous amoebic encephalitis and amoebic keratitis
Flagellates: regular flagella or kinetoplastic flagella
- Non-kinetoplastic flagellates
  - Pathogenic
    - Intestinal: Giardia lamblia and Dientamoeba fragilis
    - Genitourinary: Trichomonas vaginalis
  - Non-pathogenic
    - Intestinal: Chilomastix mesnili, Pentatrichomonas hominis
    - Oral: Trichomonas tenax
- Kinetoplastid flagellates: flagellated protozoa with DNA inside large mitochondria at one end
  - Trypanosoma species
    - Trypanosoma cruzi: causes American trypanosomiasis
    - Trypanosoma brucei: causes human African trypanosomiasis
      - Trypanosoma brucei subsp. gambiense: causes West African trypanosomiasis
      - Trypanosoma brucei subsp. rhodesiense: causes East African trypanosomiasis
      - Other subspecies have case reports of causing human disease
  - Leishmania species
    - Old World, visceralizing: L. infantum, L. donovani (in India)
    - Old World, tegumentary: L. infantum, L. donovani (Sri Lanka), L. major, L. tropica
    - New World, visceralizing: L. chagasi (genetically identical to L. infantum)
    - New World, tegumentary:
      - Viannia group (should be treated systemically): L. braziliensis, L. panamensis, L. guyanensis
      - Leishmania group (may need only local treatment): L. mexicana
Apicomplexa: gliding, sexual reproduction
- Hemosporidia
  - Plasmodium species
  - Babesia species
- Coccidia (not a microbiologically-sound category)
  - Blood and tissue
    - Toxoplasma gondii
    - Sarcocystis species
  - Gut
Ciliates: cilia
- Balantidium coli