The classis Chromadorea is monophyletic in most current analyses. However, its internal substructure is not clear. From the available data it appears that the Chromadorea comprises a number of smaller basally-branching groups and a very species-rich distal grouping. The monophyly of the basally-branching groups is currently debated, but some fundamental groupings can be defined that appear to be monophyletic clades: the families Microlaimidae and Monoposthiidae form a clade that has been named Microlaimida. The families Achromadoridae, Chromadoridae, Cyatholaimidae, Ethmolaimidae and Neotonchidae form a clade that has been named Chromadorida. The families Desmodoridae, Draconematidae and Epsilonematidae also form a monophyletic clade that has been named Desmodorida. The remaining basally-branching groups have previously been classified into a number of different "orders" (e.g. Selachinematida, Desmoscolecida or Monhysterida), however the branching pattern between these groups is unclear and the monophyly of any "orders" defined in this way is not certain. Nevertheless, taken together they appear to form a larger monophyletic clade, that I accept under the most commonly used name Monhysterida sensu lato, thus including such groups as Desmoscolecida and Selachinematida and the Comesomatidae (but not the remainder of the "Araeolaimida", as they appear to belong more distally in the tree).

The species-rich distal grouping is more problematic. It comprises three large and well-known "orders", namely tylenchids, rhabditids and spirurids. However, it also includes a significant paraphyletic stem-group of extant species, with very unclear interrelationships (like the isolaimids, partial araeolaimids, plectids, benthimermithids, leptolaimids and teratocephalids). If tylechids, rhabditids and spirurids are accepted as orders, then (in order to obtain only monophyletic orders) all the single basal branches have to be accepted as orders as well, even if they only comprise a single family or even a single species. In addition, because the interrelationship (i.e. the branching order) of the branches in the stem group are not clear, this will neccessitate changes in systematics in the future as the knowledge about the phylogeny of this clade progresses. Therefore, I accept the entire species-rich distal grouping as a single and very likely monophyletic order. Some authors use the name Rhabditida for this order, but this could lead to confusion because of the internal subgroup that is also sometimes called Rhabditida or Rhabditina. Instead I use the name Secernentea for this grouping, because this name has previously been used for all distally branching chromadoreans and at the same time avoids confusion with its subgroup Rhabditida/Rhabditina. Thus, a system of 5 orders adopted here for the Chromadorea that comprises only groups that are most likely monophyletic:

Classis Chromadorea
          Ordo Microlaimida
          Ordo Chromadorida
          Ordo Desmodorida
          Ordo Monhysterida (sensu lato)
          Ordo Secernentea