Studies using only ribosomal RNA (rRNA) genes found weak support for monophyly of the Polyporales, but more recent multilocus analyses have provided strong  evidence that the Polyporales is a clade.

The most inclusive phylogenetic analysis of the Polyporales is that of Binder et al. (2005), who sampled 124 species in the Polyporales, which they divided into four informally named subclades, the “phlebioid clade”, “Antrodia clade”, “core polyporoid clade”, and “residual polyporoid clade”. Several of these clades were not strongly supported and are regarded as provisional.

There is at present no broadly accepted, phylogeny-based formal classification of the families of Polyporales.