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A study was conducted to ascertain the taxonomic validity of the endangered taxon <i>Echinocactus horizonthalonius</i> var. <i>nicholii</i> and whether there may be other groups of populations worthy of subspecies status within the range of the species. To test the hypothesis that individuals of <i>E. horizonthalonius</i> var. <i>nicholii</i> are morphologically distinct from those of the typical variety, a multivariate analysis was done to compare the degree of morphological variation or phenotypic plasticity of stem characters within populations to the variation among populations of <i>E. horizonthalonius</i> throughout its known range. Populations of <i>E. texensis</i> were sampled for outgroup comparison. Discriminant function analysis (DFA) assigning individuals by population showed loose groupings of geographically correlated populations. The DFA assigning individuals to regions or potential subspecific taxa indicated high percentages of correct classification for individuals within populations grouped into the Chihuahuan Desert, Sonoran Desert, and Central Mexican Plateau regions. Taxonomically, these groups correspond to <i>E. horizonthalonius</i> subsp. <i>horizonthalonius</i> (Chihuahuan Desert), <i>E. horizonthalonius</i> var. <i>nicholii</i> (Sonoran Desert), and unnamed taxon of <i>E. horizonthalonius</i> (Central Mexican Plateau). Because these morphological entities are correlated with regional distributions, they are placed here under subspecies, including a newly described taxon, <i>E. horizonthalonius</i> subsp. <i>australis</i>. Because no type for <i>E. horizonthalonius</i> could be located, a neotype is designated.