Amoebae have pseudopodia as a means of locomotion and include Entamoeba histolytica in the large intestine and free-living amoebae in the CNS and eye, such as Naegleria and Acanthamoeba.
Flagellates have flagella as an organ of locomotion and include Hemoflagellates like Trypanosoma and Leishmania, Gastrointestinal parasites like Giardia lamblia, and Urogenital parasites like Trichomonas vaginalis.
Apicomplexa have a structure called an apical complex which serves as the organ of attachment to host cells and have an alternating sexual and asexual life cycle.
Apicomplexa of medical importance include Plasmodium and Babesia in blood, Toxoplasma gondii and Sarcocystis in tissue, and Cryptosporidium, Cystoisospora, and Cyclospora in gastrointestinal parasites.