Scientists at the University of Bath measured levels of fungi on platforms at 12 stations across three lines in the capital.
The research focused on penicillium chrysogenum, a common airborne fungus from which penicillin is developed.
Spore samples taken in the Underground stations were consistently higher than in two nearby outdoor locations.
They were four times the level of those at St Mary's Hospital - where Prince George of Cambridge was born on Monday.
Fungus levels on the Jubilee Line were fractionally higher than on the Central Line, at just over one fungal spore per minute of normal human breathing.
On the Bakerloo Line, which opened in 1906, passengers breathe in 0.75 fungal spores per minute.
The study, published in Fungal Ecology, focused on penicillium chrysogenum, first discovered by Alexander Fleming in 1928 at St Mary's Hospital.
Fleming's discovery led to the breakthrough development of penicillin as an antibiotic.
While the Jubilee Line had high levels of fungal spores, it had the lowest proportion of penicillium spores, suggesting other fungi are responsible.
Dr Daniel Henk, lead researcher, from the University of Bath's Department of Biology & Biochemistry, said: "Finding an abundance of fungi in the air of the London Underground is not that surprising because people encounter them nearly everywhere all the time.
"However, our observation that part of the fungal community differs between the above ground and below ground air and between Underground lines suggests that the physical structure of the Tube is more than a sieve through which airborne fungi flow.
"In some ways, the Underground might be like the U-bend of a sink for the air around the people of London, trapping fungi in the air from outside, but it is also an environment capable of supporting fungal growth in its own right. Uncovering the fungal species in the built environment should ultimately help us manage our building for sustainability, health and biodiversity."
During the research, two new penicillin species were identified, penicillium floreyi and penicillium chainii.
They have been named after Howard Florey and Ernst Chain, who won the Nobel Prize for Medicine, along with Fleming, for their work on penicillin.