The Palnyothèque is in theory an extension of the Histothèque, but historically developed separately from the latter, in far more recent times. It contains spore (Fern) and pollen (Phanerogam) slides.

The slides in the Palynothèque collection were mainly made following the technique developed by the Swedish palynologist Gunnar Erdtman in 1952. The material (fresh, fixed or even taken from the herbaria) is processed using aggressive chemical agents (acetylosis), so that only the outer coating (exine) of the spore or pollen grain is preserved. The shape is preserved, the coating is transparent and any ornamentations (striations, thorns, etc.) are thoroughly cleaned. The objects, mounted in gelatin and glycerine, can be studied through a microscope, usually with a high enlargement factor (x 1,000). This requires the use of thinner, more fragile glass slides than for anatomy. Their appearance is very similar to that of fossils, which makes comparisons much easier, particularly in geological research. The slides are perfectly standardised and lend themselves to large-scale production here, which helps with exchanges and loans. It currently includes around 40,000, as well as photographic collections (palynological atlases, details through scanning transmission electron microscope), and reports on certain slide series, some previously unpublished. The slides in the general series, which are frequently borrowed and consulted, are stored by chronological order of creation.

The Palynothèque is a merger of two collections, both created at the Muséum but with different goals. The oldest dates back to 1959 (but the oldest slides date back to 1955) and was founded by Madeleine Van Campo, the pioneer of modern palynology in France, and continued to expand until 1996, under the leadership of M.-T. Cerceau-Larrival (CNRS): its aims were pollinic morphology, the study of the evolution of more temperate Angiosperm groups (Saxifragales, Apiaceae), and certain applications for agronomy (pollen banks), apiculture and allergology. The other collection was created by A. Le Thomas (EPHE) in 1970 and specialised in the study of the tropical groups (taxonomy and phylogeny). It is therefore directly linked to the herbaria, particularly the type specimens.

The Palynothèque therefore provides abundant comparison material for all identification of current or fossilised pollen on a worldwide scale, as well as for the theoretical study of pollinic morphology and its evolution. Interest in the collection has been rekindled in the last few years by research into the development of pollen grains in relation to their evolution (known as "evo-devo").