The genus Watsonia was named by Philip Miller, who worked as a Curator of the Chelsea Physic Garden, in honour of his friend Sir William Watson (1715–87), who was a physician and naturalist from London. This species is named after Miss Edith Struben (1898–1936), a botanical illustrator and painter, who collected specimens near Sabie and sent the plants to Kirstenbosch National Botanical Garden in 1930, which later flowered and formed the type collection. This species belongs to the Iridaceae, known as the iris family. Most watsonias are adapted to Mediterranean climate conditions (cool wet winters and hot dry summers), with few, including this species, being adapted to summer-rainfall climates.

Watsonia strubeniae was first collected in the 1920s near Pilgrim's Rest by both F.A. Rogers and G. Roe, working independently. Roe's specimen was labelled Watsonia roei in N.E. Brown's handwriting, but Brown passed away before he could formally publish the name and description. In 1926, Louisa Bolus described this species as a W. transvaalensis var. drakensbergensis, based on collections made by Rogers and Roe. In 1930 Bolus sent the plant to Kirstenbosch National Botanical Garden, those plants later became the type collection. By 1931, Bolus had also described W. strubeniae from a later collection, not realizing that it had already been named, at least as a variety of W. transvaalensis.

In 1938, Cape botanist G.J. Lewis introduced the synonym Watsonia alpina, distinguishing it from W. strubeniae due to its less dense spike and bracts that do not clasp the stem. However, more recent findings suggest these differences may not be significant, implying that Lewis’s separation of the species may have been inaccurate. 

Watsonia strubeniae is closely related to Watsonia transvaalensis, but they can be distinguished by several features. W. strubeniae has small, pale pink flowers with a short perianth tube measuring 7–9 mm and tepals that are 17–19 mm long. It possesses short, dry bracts (9–14 mm) that do not clasp the stem, along with a branched stem and broader leaves with thickened margins. In contrast, W. transvaalensis exhibits larger flowers with tepals measuring 20–25 mm and longer bracts (13–28 mm). Its leaves are narrower with lightly thickened edges, and the stem is usually unbranched. W. transvaalensis is found between Graskop and Haenertsburg, while W. strubeniae occurs further south, around Sabie and Pilgrim’s Rest.