The Paleobotanical Collection was founded by Louis Agassiz (1807–1873) based on European collections that were part of the Museum of Comparative Zoology. It was enhanced by a donation from the Boston Society of Natural History in the 1890s and shortly thereafter was transferred from the Museum of Comparative Zoology to Harvard’s Botanical Museum.

The collection includes about 60,000 specimens and is the second largest repository for fossil plants in the United States. The collection, without peer for completeness of stratigraphic, geographic, and taxonomic coverage, is also rich in European material not available elsewhere in the United States. An extensive collection of several thousand samples of coal and related material are also part of the collection.

Fossil pollen and spores are part of the pollen collections, the most notable being material from the Oligocene Brandon Lignite of Vermont, USA, prepared by Alfred Traverse, and Holocene pollen and spores from Gatun Lake, Panama, described by Alexandra Bartlett. The Precambrian material collected by Elso Barghorn and Andrew Knoll is of major importance.

Our palynological collection of living plants includes about 11,000 specimens of extant vascular plants, especially from tropical America and China. To aid in the identification of fossil seeds, a small collection of fruits and seeds from modern plants has also been developed.