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Trillium and Trillidium are both individually and collectively monophyletic, it is a matter of choice whether or not to recognize genus Trillidium.

Excluding the segregate taxa listed above, the remaining taxa separate into four clades with the following names:

* Trillium subgen. Trillium
* Trillium subgen. Callipetalon
* Trillium subgen. Delostylis [as Delostylium]
* Trillium subgen. Sessilia [as Sessilium]

Traditionally, Trillium subgen. Trillium has included

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