Phylum [Choanozoa] Cavalier-Smith, 1981
   1 Class Mesomycetozoea Ajello & Mendoza, 2000 see Class Ichthyosporea Cavalier-Smith, 1998
   2 Class Corallochytrea Cavalier-Smith, 1995 see Order Corallochytrida Cavalier-Smith, 1995
   3 Class Choanoflagellatea Cavalier-Smith, 1998