Sea urchins belong to the phylum Echinodermata - a phylum which also includes sea stars, brittle stars, and sea cucumbers. Most notably, this means, like all echinoderms, sea urchins have primary bilateral symmetry, and unique secondary five-fold symmetry. This symmetry, though often difficult to recognize on the live animal, can be easily identified in its internal anatomy and on the tests of dead urchins. All echinoderms also have tube-feet: a unique adaptation that utilizes water pressure in a suction-like system - the water vascular system - for locomotion, feeding, and respiration.

Both sea urchins and sea cucumbers belong to the subphylum Echinozoa, distinguished by their blob-like shape, lacking 'arms' like sea stars and brittle stars.

The class Echinoidea encompasses all true urchins, unique for having their iconic hard, typically global and spine-covered tests, the 'shells' of urchins (Smith and Pier).