In 1993 Cavalier-Smith described the sarcomonads as a subclass known as “Sarcomonadia”, an assemblage of unrelated cercozoans (thaumatomonads, proteomyxids, cercomonads...) and excavates (jakobids), in the now defunct class “Heteromitea”, in the old phylum “Opalozoa”. This subclass was created to lump together protozoa that have an anisokont type of zoospore (i.e. two cilia of different lengths), are non-thecate and have isodiametric extrusomes.^[2] Sarcomonadia was composed of three superorders:

1. “Jakobidea” (orders Jakobida and Cercomonadida), made up of sarcomonads with a single Golgi dictyosome;
2. “Thaumatomonadidea” (order Thaumatomonadida), with scales made in vesicles associated with the mitochondria;
3. Proteomyxidea (orders Pseudosporida and Leucodictyida), made up of sarcomonads with an unusual intranuclear rod of microfilaments unseen in other protists.^[2]

Phylogenetic analyses published in 1997 showed close relationships between filose and reticulose amoebae and zooflagellates such as the sarcomonads, and they were grouped under the provisional phylum Rhizopoda.^[4] In here, the sarcomonads were grouped as the class Sarcomonadea inside the subphylum Monadofilosa, and Sarcomonadea was emended to exclude the proteomyxids and jakobids.^[5]

Later, in Cavalier-Smith's A revised six-kingdom system of life of 1998, the phylum Cercozoa was created to formally establish this group of protists previously known as Rhizopoda. This discovery put an end to the taxonomical dichotomy between amoebae and flagellates, since they are phylogenetically intermingled in Cercozoa.^[6]

In 2003 the term Sarcomonadea was emended again to contain only two orders:

1. Metopiida, comprising the single species Metopion fluens, but was later moved into a different class;
2. Cercomonadida, the first current sarcomonad order, comprising the families Cercomonadidae and Heteromitidae.^[3]

In 2009 the problematic Heteromitidae were broken apart and rearranged into the second current sarcomonad order Glissomonadida.^[7]

In 2012 the paracercomonads joined Sarcomonadea, initially as cercomonads^[8] and later as the third current sarcomonad order Paracercomonadida.^[1] At the same time, the superclass Ventrifilosa was created to comprise Sarcomonadea, Imbricatea and Thecofilosea.^[8] That same year, the protist Katabia was added to Sarcomonadea but remained incertae sedis within the group.^[9]

The class Sarcomonadea is most closely related to Imbricatea and Thecofilosea. Together, they form the superclass Ventrifilosa in the phylum Cercozoa. The current classification divides the class into three orders: paracercomonads (subclass Paracercomonada), cercomonads and glissomonads (subclass Pediglissa).^[1]

Class Sarcomonadea Cavalier-Smith, 1993 stat. nov. 1995 emend. 2018
 Subclass Paracercomonada Cavalier-Smith, 2018
  Order Paracercomonadida Cavalier-Smith, 2018
   Family Paracercomonadidae Cavalier-Smith, 2012
 Subclass Pediglissa Cavalier-Smith, 2018
  Order Cercomonadida Poche, 1913 emend. Cavalier-Smith
   Family Cavernomonadidae Cavalier-Smith, 2012
   Family Cercomonadidae Saville Kent 1880-1881, emend. Cavalier-Smith
  Order Glissomonadida Howe et al., 2009
   Suborder Allapsina Cavalier-Smith, 2018
    Family Allapsidae Howe et al., 2009
   Suborder Sandonina Cavalier-Smith, 2018
    Family Bodomorphidae Hollande, 1952
    Family Sandonidae Howe et al., 2009
    Family Proleptomonadidae Howe et al. 2009
   Suborder Pansomonadina Vickerman, 2005 stat. nov. Cavalier-Smith, 2018
    Family Viridiraptoridae Hess & Melkonian, 2013
    Family Agitatidae Cavalier-Smith & Bass, 2009
    Family Acinetactidae Stokes, 1886
    Family Aurigamonadidae Cavalier-Smith, 2011
 Sarcomonadea incertae sedis
  Family Katabiidae Cavalier-Smith, 2012