The characters useful for identifying ascidians and understanding them and their phylogenetic relationships include the consistency of the test and surface markings, position and orientation of the apertures, habit of the organism, organisation of zooids in the colony, relative sizes of the thorax, abdomen, and posterior abdomen (if present), branchial tentacles, opening of the neural gland on the dorsal tubercle, dorsal lamina (plain membrane or languets), siphonal spines, muscles (position, number, inner and outer layers), branchial sac and internal longitudinal vessels, branchial (pharyngeal) folds, the shape of the perforations (stigmata), the position and course of the gut and its sub-divisions, the nature of any gut diver-ticulae (liver), anal border, condition of the stomach wall, presence of a kidney, the position and type of gonads, and aspects of the larvae including adhesive organs, ectodermal ampullae, trunk size, and the presence of blastozooids.

Ascidians are contractile and contraction directly affects the appearance and consistency of the test and shape of both solitary individuals and colonies. Conformation of cloacal cavities and zooid systems (in life maintained by positive internal pressure of incoming ciliary currents) are obscured as colonies collapse on fixation. Colour also is lost following removal from the substrate and as fixative and preservative are added. The morphology of many internal organs, especially in small colonial zooids are obscured, particularly the number and appearance of muscle bands, branchial vessels and stigmata. Gonads are sometimes ephemeral and age and maturity can dramatically affect their appearance. Also, in these organisms there is a wide range of intraspecific variation and both individuals and colonies and are affected by environmental factors. For these reasons ascidians are often difficult to identify.

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