The Mendocino cypress differs little from "C. goveniana" in morphology, with the most conspicuous difference in herbarium material being the usually glossy black seeds, unlike the dull brown seeds of "C. goveniana", but even this character is not constant, with dull brown seeds found in the southernmost populations of "C. pigmaea" near Point Arena. Preliminary genetic studies have shown some differences, with notably some plastid sequences ("matK", "rbcL", and "trnL") suggesting a possible closer relationship to "C. macrocarpa", though other sequences confirm its close relationship to "C. goveniana". In cultivation together with "C. goveniana", it retains a very different crown shape, with a tall slender crown, contrasting with the broad, shrubby crown of "C. goveniana"; it also has darker green foliage (paler, yellow-green in "C. goveniana").