Palynology is the study of spores and pollen, has many applications in botany, geology and medicine. Spores are primitive reproductive bodies of fungi and some plants. Pollen grains are small male reproductive bodies produced and dispersed by seed plants. Spores and pollen are small (5-100 um), spherical or oblong structures, identifiable under a compound light microscope. Fine details of wall structure and sculpturing can be seen under the scanning electron microscope (20 000 to 40 000 magnification). The detailed structure of the wall (exine layer), and the number and arrangements of pores and furrows in the wall, are the diagnostic characters used in identification. Pollen is a key tool in reconstructing past vegetation and environments (palaeoecology), because the outer wall is both extremely resistant to decay and elaborately and beautifully constructed so that identification to species or family level is possible. Pollen of many plants is discharged into the air annually and falls into lakes and bogs as a "rain" which represents the surrounding vegetation. Many forest regions in Canada produce a total pollen fallout of 30 000 to 60 000 grains per cm2 annually, while tundras produce fewer than 1000.

Pollen is preserved in lake or bog sediments that accumulate each year. This preservation results in a sequence of pollen assemblages representing the succession of past vegetation. For example, Tertiary sediments 10-20 million years old, under the Mackenzie Delta, NWT, contain deposits of spores which indicate that a rich coniferous forest grew there, similar to modern forests in coastal BC and Washington. Analysis of the spore content of such rocks is used in the search for fossil fuels and the petroleum industry employs palynologists as part of this exploratory activity. Pollen analysis of sediments that have accumulated since the end of the latest glaciation reveal the vegetation changes and tree migrations that have produced the present vegetation of Canada.

In addition to showing the responses of vegetation to climatic change, pollen data indicate effects of human cultures such as clearing, burning and agriculture. A pollen record from a small lake near Toronto shows evidence of maize cultivation (1380 AD) in an Iroquoian village near the site, and evidence of forest clearance. The same site shows the beginning of European agriculture by the abrupt rise in frequency of ragweed pollen. Palynology is used in quality control tests of honey to identify the source plants used by bees, and it has been used in forensic science to solve crimes (eg, when pollen adhering to clothing can indicate the scene of a crime).