The relationships of the Sphenophyta to other plant taxa are not well understood. The Sphenophyta form one of three main branches of the "trimerophyte" lineage of vascular plants, the other two being the Pteridopsida (ferns) and the progymnosperm line. Which one of these is closer to the Sphenophytes is not yet known. The situation is made more complex by the existence of several Devonian fossil plants (such as the Cladoxylales) that appear to be related to these lineages in some way, but whose exact affinities have not been worked out.

Sphenopsids have traditionally been divided into three orders: Pseudoborniales, Sphenophyllales, and Equisetales. The latter group comprises the archaeocalamites, calamites, and horsetails. The genus Ibyka is not placed in the Sphenophyta by all paleobotanists; they may be closer to ferns or early fern-like plants such as the Cladoxylopsida.

Note that because they often work with dismembered plant organs rather than whole plants, paleobotanists have given form names to fossil plant organs. We have given some of the most common Latin genera with each group, including both whole plant genera and form taxa.