Four major groups of protozoa are recognised and often given the status of phylum. Note, however, that in the animal kingdom proper (Metazoa ), phyla are distinguished on their different body plans and that no comparable body plans are found in Protozoa.
The groups are:
flagellates (or Mastigophora) amoebae (or Sarcodina) sporozoans (or Sporozoa, Apicomplexa) and ciliates (or Ciliophora).
The above classification represents a convenient filing system. We now know from molecular data (especially gene sequencing), that the different groups of flagellates and amoebae are not closely related and that there may be much greater genetic distance between two groups of flagellates than between flowering plants and vertebrates.
The above classification is not therefore phylogenetic (i.e. reflecting the course of evolution). It is at present premature to try to construct a phylogenetic classification of protists, and for purposes of identification the above traditional classification is a starting point.