Originally limited to a small group of species with relatively large, short-tubed flowers with radially symmetric perianth, Tritonia now also includes species with short- to long-tubed, zygomorphic flowers. It forms part of a small clade of genera including Dierama, Duthiastrum, Ixia and Sparaxis defined by netted corm tunics, mostly radially symmetric flowers, more or less dry and papery or membranous bracts, and specialized, subglobose seeds with a smooth, glossy testa and a raphal vascular bundle excluded from the seed body during ripening. Tritonia is immediately related to Dierama and Ixia, the latter also often with 3-toothed bracts. Tritonia is separated from these two genera by its more sturdy and firm (not wiry) stem, leaves usually with specialized margins lacking a vascular bundle and having instead columnar epidermal cells with thickened walls, and possibly ancestrally zygomorphic flowers, often with the main vein on some or all lower tepals thickened or raised in a fleshy or bony callus or tooth. Similar teeth are developed elsewhere only in some species of Lapeirousia and Afrosolen (tribe Watsonieae). In several species the perianth is thin-textured with prominent, dark veins. Most species have a basic chromosome number of x = 11 (exceptionally x = 10).

Four species are anomalous in the genus in their leaf anatomy, possessing a marginal vascular trace with associated sclerenchyma cap and lacking the specialized, thickened epidermal cells that are characteristic of the other species of Tritonia (see De Vos, 1982b). These are the two Richtersveld endemics, T. delpierrei and T. marlothii, with narrow, leathery or subsucculent leaves, and two that have narrow, essentially centric leaves, T. bakeri, with stiffly linear, compressed elliptical or subterete leaves; and T. kamisbergensis with wiry, terete and fibrotic leaves.

Relationships among the species have not been tested using molecular sequences. We assume that the genus is ancestrally zygomorphic by analogy with other genera of Crocoideae containing species with both actinomorphic and zygomorphic flowers. In light of its close relationship with Dierama and Ixia, both of which have ancestrally radially symmetrical flowers, this assumption remains to be confirmed.

De Vos (1982, 1983) initially grouped the species into five sections, referring the majority to sect. Montbretia, defined by zygomorphic flowers with one or all of the lower tepals bearing a well-developed, tooth- or axe-like crest or callus on the midline near the base. Previously segregated at generic rank, this section is widely distributed from southern to south tropical Africa, and comprises three distinct groups of species identified by De Vos as possible subsections. The largest included nine species with orange to yellow or pink to red, strongly bilabiate flowers with large, axe-like calluses on the lower tepals. A second group included two species from the Richtersveld with subsucculent leaves without thickened marginal epidermis and pale, salver-shaped flowers, T. delpierrei and T. marlothii. The remaining two species, T. florentiae and T. karooica from the western central karroid zones of South Africa, were considered taxonomically distantly related by De Vos but both share similar long, crest-like calluses on the lower tepals and unusually large capsules.

Sect. Tritonia included four species with short-tubed, bowl-shaped, orange or pink flowers with a radially symmetrical perianth lacking well-developed calluses on the lower tepals, and with central or loosely unilateral stamens. One of the species included here, T. dubia, is almost certainly misplaced, differing from the other species in its ± rotate flowers with erect, symmetrically disposed stamens inserted near the top of the perianth tube, and larger, ellipsoid capsules. Similar capsules are found in T. laxifolia and T. moggii (sect. Montbretia), suggesting an alliance with those species. All members of sect. Tritonia are local endemics of southwestern South Africa.

The remaining species in the genus have zygomorphic flowers, usually without tepal calluses. The monotypic sect. Teretifoliae included just Tritonia kamisbergensis from Namaqualand, distinguished by its fibrous, subterete leaves, small, subherbaceous bracts, and red flowers. Sect. Pectinatae included four species with a dense, almost horizontal spike of pale pink to cream or white flowers with an elongate perianth tube. Three are fynbos endemics with uniquely modified leaves that develop longitudinal, flange-like outgrowths from the adaxial surface and margins. The fourth, T. tugwelliae from the western Great Karoo, has conventional plane leaves and small, uniformly pale bracts without dark upper margins and is thus evidently misplaced here. The residue of the species are accommodated in sect. Subcallosae, which was poorly and essentially negatively diagnosed as lacking the distinctive features of the other sections. The distinction between sect. Subcallosae and sect. Montbretia is, however, blurred by T. pallida, which sometimes has large, axe-like calluses on the lower tepals, and the two sections were combined by De Vos (1999). The species in sect. Subcallosae fall into two distinct groups based on flower shape: one with pale, long-tubed flowers restricted to the winter-rainfall region of South Africa, and a second with yellow or orange to red, funnel-shaped flowers, mainly from the eastern seaboard and near-interior. The long-tubed T. bakeri is anomalous in the section in its centric, terete or compressed leaves without true margins and its association with the other long-tubed species in the group may be mistaken.