Edvard August Vainio was a world-renowned Finnish lichenologist. In Finland, however, he was a controversial person due to his strong pro-Finnish political views. Equally disputed was his opinion that systematics should be based on evolutionary theory and phylogenetic thinking. Vainio was familiar with the ideas of the early German phylogeneticists—especially those of Carl Wilhelm von Nägeli – and, applying them, aimed to create an exact method for building a natural classification of lichens already at the end of the nineteenth century. In this respect, Vainio was a true pioneer, as no actual phylogenetic method had yet been developed. In the general spirit of the time, Vainio focused on finding the ancestors of species and other taxa by comparing primitive and derived features of homologous characters. However, Vainio already understood the concept of sister groups in 1880, the identification of which is the basis of all modern phylogenetic research. Nevertheless, the distinctive method developed by Vainio was not so much focused on the construction of a phylogenetic tree, but on revealing the origin of species through the differentiation and fixation of their polymorphic variation. Indeed, Vainio’s species concept is surprisingly similar to the phylogenetic species concepts presented a hundred years later. Although in many ways progressive, Vainio’s views did not influence the development of phylogenetics more widely, but his discussions are nevertheless a valuable source to understanding the early development of phylogenetic theory.