The following unranked classification of eukaryotes is intended to serve as a guide to sort out where traditional protozoology groupings have ended up with respect to current phylogenetic views. It is based on my own attempts to simplify the classification used for GenBank as of 9/01, with the traditional names colored as follows (following Hickman et al., 11th ed., Integrated Principles of Zoology, pp. 236-237, with "*" indicating poly- or paraphyletic groups, according to those authors):

Protozoa

Phylum Sarcomastigophora*
     Subphylum Mastigophora*
         Class Phytomatigophora* (plant-like flagellates)
         Class Zoomatigophorea* (flagellates without chloroplasts)
     Subphylum Opalinata (parasitic, e.g., Opalina)
     Subphylum Sarcodina* (have pseudopodia)
       Superclass Rhizopoda*
         Class Lobosea*
         Class Eumycetozoea*
         Class Filosea
         Class Granuloreticulosea
       Superclass Actinopoda
         Class Acantharea (have strontium sulfate skeleton)
         Class Polycystinea (most have siliceous skeleton)
         Class Phaeodarea (have skeleton of mixed silica and organic matter)
         Class Heliozoa (axopodia radiating on all sides, mostly freshwater)
Phylum Labyrintomorpha
Phylum Apicomplexa (have apical complex organelle at anterior end)
         Class Sporozoa (e.g., Toxoplasma, Plasmodium)
Phylum Microspora (=Microsporidea, parasites of arthropods and some vertebrates)
Phylum Ascetopora (parasites of arthropods and a few vertebrates)
Phylum Ciliophora (ciliates, with cilia or ciliary organelles, micro- and macronuclei)

Eukaryota (organisms with cell nucleus)

Acanthamoebidae (e.g., Acanthamoeba)
Acantharea
Alveolata (alveolates)

Apicomplexa (apicomplexans)
Ciliophora (ciliates)
Dinophyceae (dinoflagellates)

Cercozoa
core jakobids
Cryptophyta (cryptomonads, incl. Chilomonas)
Diplomonadida (diplomonads)
Entamoebidae (incl. Entamoeba)
Euglenozoa

Diplonema
Euglenida (euglenids, incl. Euglena)
Kinetoplastida (kinetoplasts)

Fungi/Metazoa group

Fungi (fungi)
Choanoflagellida (probably sister taxon of Metazoa, e.g., Codosiga)
Metazoa (metazoans, e.g., multicellular animals, some authors include Myxozoa)

Granuloreticulosea

Foraminifera (foraminiferans = "forams", incl. ? testate amoebas (Arcella, Difflugia) (links: 1 - 2 - 3 - 4 - note 1)

Haptophyceae
Heterolobosea

Acrasida
Schizopyrenida (incl. Naegleria)

Lobosea

Gymnamoebia (incl. Amoeba, Chaos)
Leptomyxida

Malawimonadidae
Microsporidia
Mycetozoa

Dictyosteliida (dictyostelid cellular slime molds)
Myxogastria
Protostelida

Oxymonadida
Parabasalidea (parabasalids)

Hypermastigida
Trichomonadida (trichomonads)

Paramyxea
Pelomyxidae
Plasmodiophorida (plasmodiophorids)
Polycystinea
Rhodophyta (red algae, multicellular)

Bangiophyceae
Florideophyceae
Goniotrichales

stramenopiles (heterokonts)

Bacillariophyta (diatoms)
Bicosoecida
Blastocystis
Bolidophyceae
Chrysomerophyceae
Chrysophyceae (golden algae)
Developayella
Dictyochophyceae
Eustigmatophyceae
Hyphochytriomycetes
Labyrinthulida
Oikomonadaceae
Oomycetes
Pelagophyceae
Phaeophyceae (brown algae, multicellular)
Phaeothamniophyceae
Raphidophyceae
Slopalinida
Xanthophyceae (yellow-green algae)

Viridiplantae (green plants)

Chlorophyta (unicellular green algae, e.g., Volvox, multicellular green algae)

Streptophyta (multicellular stonewarts, land plants, etc., derived from Chlorophyta)

 

Note 1: I searched GenBank for about 20 testate amoeba generic names and found only Gromia, which is listed with forams. I find it surprising (or suspicious) that noone appears to have sequenced any of these yet!