[1] Sargent thought that the distinctness of the seeds from those of C. goveniana definitively showed it to be a species though its growth habits and form did not make it easy to identify.

In the 20th century some treated Cupressus pygmaea as a distinct species, following Sargent, including Wolf (1948),[4] Griffin & Critchfield (1976),[8] and Lanner (1999).

pygmaea (Lemmon) A.Camus), including Camus (1914),[10] and the Jepson Manual (1993),[11] and one publication, the Flora of North America, did not distinguish it at all within C. goveniana.

In the pygmy forest plant community on poor, acidic, nutrient-starved podsol soils with drainage impeded by an iron hardpan, it is a stunted tree from 0.2–5 meters in height at maturity.

When growing on deep, well-drained soils it can be a large tree up to 30–50 meters in height and 1–2.4 m in trunk diameter.

[11] The Mendocino County official soils survey states that "While not formally recognized as a major forest cover type, the coastal portion of the survey area also includes bishop pine and Mendocino cypress (pygmy) forest types".

[14] Along the Mendocino coastal terraces, whose geological age is approximately one million years, studies have been conducted of the biomass density and primary productivity of the Hesperocyparis pygmaea-dominated pygmy forest.

In the Mendocino cypress pygmy forests, biomass was measured to range between 1.6 and 4.4 kilograms per square meter aboveground; moreover, net primary productivity was found to measure 180 to 360 grams per square meter per annum above the ground surface.

According to Westman, productivity of the H. pygmaea forest lies within the range expected for open, dry woodlands.