Young Vainio's friendship with university student Johan Petter Norrlin, who was nearly eleven years older, helped him develop an impressive knowledge of the local cryptogams (ferns, mosses, algae, and fungi, including lichens) and afforded him ample opportunity to hone his collection and identification techniques at an early age.

Disillusioned with his prospects for permanent academic employment, and faced with the reality of having to provide for his family, he was obliged to accept a position with the Russian censorship authority, which led to his ostracism by the Finnish scientific community.

[21] Another early publication, Adjumenta ad Lichenographiam Lapponiae fennicae atque Fenniae borealis ("Adjustments to the lichens of Finnish Lapland and northern Finland"; published in two parts in 1881 and 1883) was based on material he had collected in 1875 and 1877 in desolate locations near the border of the Grand Duchy of Finland and Russia, including North Karelia, Kainuu, Koillismaa, eastern Lapland, and Russian Karelia.

In these works—considered the earliest publications on phytogeography in the Finnish language—Vainio meticulously catalogued the moisture, light, and soil conditions of the places where he collected, and defined terms that would eventually become standard terminology in the field.

[27] As noted by Adolf Hugo Magnusson in his 1930 obituary of Vainio, the characteristics that would represent his later work were evident already in these early publications: the keen observations, the detailed descriptions and the careful study of the specimens in question.

To write special botany in Finnish goes out as if a Frenchman would deliver such a work in Breton or Basque or another of the dialects of the 12 tribes, which jointly constitute the French nation.

Titled Tutkimus Cladoniain phylogenetillisestä kehityksestä ("An Investigation on the Phylogenetic Development of the Cladoniae"), this work was the first dissertation on natural science that was published in the Finnish language.

[32] According to his colleague and biographer Kaarlo Linkola, "this paper of 62 printed pages was sensational on account of its modern theme, as well as its youthful freshness and its originality".

[33] Vainio supported the theory of evolution in his work, and proposed that the science of systematics required an examination of phylogeny, rather than mechanical categorization based on sometimes superficial characters.

Such a radical outlook was viewed with some reservation by Johan Reinhold Sahlberg (docent in entomology) and Sextus Otto Lindberg (Professor of Botany), who were charged with assessing Vainio's work.

[44] After being granted a stipend from the University, in 1885 Vainio undertook a year-long expedition to Brazil, collecting primarily lichens in the vicinity of Rio de Janeiro and in Minas Gerais.

"[46] In Rio de Janeiro, Vainio met the French botanist, and later landscape designer for Brazilian royalty, Auguste François Marie Glaziou, who advised him on possible travel routes.

Germain advised Vainio against travelling via his originally intended route, and convinced him instead to visit the biodiverse Caraça Mountains [pt], north of Ouro Branco.

For example, Vainio was sent for identification the collections of Portuguese botanist and army doctor Américo Pires de Lima [pt], who made them as part of a military campaign in Mozambique during 1916–1917.

[73] Because the department Chair, Sextus Otto Lindberg, did not trust his Finnish-language skills sufficiently to be able to judge the merits of Vainio's work, other opinions were sought, and so in addition to William Nylander, Theodor Magnus Fries and Johann Müller were recruited.

This is a matter that may be possible and explainable in Finland (and unfortunate is that such is the situation) but in the common practical world, here in the logical humanity, such a thing is impossible even to mention without incurably injuring the person concerned.

[76] Suspecting that he had been discriminated against in the selection of a professor, Vainio appealed the decision, arguing that the expert opinions came from representatives of an "openly hostile" school that was prejudiced towards him, and further, that he was the only one of the applicants with the ability to lecture fluently in both Finnish and Swedish.

[82] Norwegian botanist Per Magnus Jørgensen suggests that not only did Vainio's support of Schwendener's theory cost him a position as professor, but probably also influenced the choice of author for the lichen section of Adolf Engler and Karl Anton Eugen Prantl's influential monograph series Das Pflanzenreich—a job awarded to the then relatively unknown Austrian lichenologist Alexander Zahlbruckner.

[83] Finnish historian Timo Tarmio suggests that Vainio's failure to secure a professorship must have been a further blow to him personally because, like Norrlin, his older brother Joel Napoleon Lang had successfully pursued a university career as a professor in the Faculty of Law.

[42] Faced with the reality of securing stable employment to provide for his wife and four children,[85] Vainio accepted a job as a censor in the press service of Helsinki in 1891, a position in which he was appointed superintendent in 1901.

[39] For example, despite their innovativeness and importance, Vainio's early publications on phytogeography in the border regions of northeast Finland and Russian Karelia were rarely cited by his Finnish colleagues, largely for political reasons.

[87] Shortly after the turn of the century, when Finland's constitutional struggle dominated the political landscape, students refused to enrol in his course as a form of protest against his chosen profession.

His last entry was to name and describe Lecidea keimioeënsis (collected by Linkola in Keimiötunturi [fi]) as a new species, when his illness suddenly forced him to stop work and hurry to the hospital.

[44] Vainio was generally healthy for most of his life, but near the end he suffered from severe nephralgia (pain in the kidney) and spent his final three weeks in the hospital of Turku.

[114] Finnish-speaking experts had admired Vainio's dissertation, but his international reputation as a prominent lichenologist was first established by his floristic treatment of the lichens collected during these trips documented in the Adjumenta, published in Latin in 1881 and 1883.

These ideas would persist into the first half of the 20th century, largely due to the publication of Zahlbruckner's influential Catalogus series, issued in ten volumes from 1922 up until 1940, which was based on these old views.

[122] It was at the International Botanical Congress in Stockholm in 1950 that Rolf Santesson advocated for Vainio's ideas and presented an integrated classification for fungi and lichens based on an updated system developed by John Axel Nannfeldt.

Although some other influential lichenologists took a conservative view and lumped Pseudocyphellaria with Sticta (such as Zahlbruckner in his Catalogus Lichenum Universalis), Vainio's concept of the genus prevailed and has been used extensively for over a century.

[131] In his 1931 memorial address, Alvar Palmgren, then President of the Societas pro Fauna et Flora Fennica, recalled that many of Vainio's scientific papers appeared in the Society's publications and were among the best of them.

"[135] In 1997, a symposium on Vainio and his work was organised in Brazil by the Grupo Latino-Americano de Liquenólogos (Latin-American Group of Lichenologists) and the International Association for Lichenology.