The presented studies are focused on the comparative morphological and anatomical analyses of two wormwood varieties, i.e. the typical variety Artemisia absinthium var. absinthium and var. calcigena, endemic to the Pieniny Mountains (Western Carpathians). The studies comprise descriptions of the characteristics of pollen grains and the achene surface, analyses of seed germination rate and slime formation, stem anatomy, and leaf morphology and anatomy. The pollen grain surface is typical for the whole Artemisia genus. The seed coat consists of proper epidermal cells and slime cells, whose presence is related to the ability to form slime in both taxa. The obtained results show some typical xeromorphic features in the stem and leaf structure, which are more strongly pronounced in A. absinthium var. calcigena than in var. absinthium. These features include a continuous periderm layer and lignified pith cells developed in the early stages of growth. Although some differences between the studied taxa exist (e.g., better germination power, number of flower heads, length of pedicels and anatomy), they are rather a manifestation of phenotypic plasticity and habitat influence than the taxonomic identity. Based on the results we can state that A. absinthium var. calcigena presents a low position as an independent taxonomic unit and may exemplify a local phenotypic form.