As a member of the basal echinoid order Cidaroida, its morphological, developmental and molecular genetic characteristics make it a phylogenetically interesting species.

During daylight hours, the slate pencil urchin uses its large primary spines to anchor itself under or atop rocks or to lodge itself in crevices.

[12] When its development is contrasted to the cidaroid sister subclass Euechinoidea, E. tribuloides becomes a very interesting organism from the standpoint of developmental and evolutionary biology.

In euechinoid embryonic development, e.g. in the purple sea urchin, the micromeres comprise a set of four small cells that reside at the base of the vegetal plate.

They are a "precociously invaginating lineage", meaning that they move into the blastocoel just prior to gastrulation; these four cells then eventually give rise to the larval skeleton.