There are as many as 20,000 different kinds of lichen known, and new ones being discovered all the time. These are treated as species by lichenologists, but are not species in the same sense as animal or plant species. Because lichens are formed through a combination of alga and fungus, it is not possible to study the phylogeny of lichens, per se. Rather, the relationships of the fungal partner and the algal partner must both be studied.
The algal partner is usually a unicellular pleurastrophycean green alga, such as Trebouxia, Pseudotrebouxia, or Myrmecia, or is often a cyanobacterium, such as Nostoc or Scytonema. The fungal partner may be an Ascomycete or Basidiomycete.
Current work on the systematics of lichens is focussed on the question of the origin of lichens, and particularly to answer "How many times have lichens originated among fungi?" We know that lichens have developed independently in the Ascomycota and Basidiomycota, but no one is entirely certain how many times lichenization has occurred in each of these groups.
For more information on the systematics of lichen fungal partners, visit the Tree of Life