Background Recent decades have seen a major surge in the study of interspecific variation in functional traits in comparative plant ecology, as a tool to understanding and predicting ecosystem functions and their responses to environmental change. However, this research has been biased almost exclusively towards vascular plants. Very little is known about the role and applicability of functional traits of non-vascular cryptogams, particularly bryophytes and lichens, with respect to biogeochemical cycling. Yet these organisms are paramount determinants of biogeochemistry in several biomes, particularly cold biomes and tropical rainforests, where they: (1) contribute substantially to above-ground biomass (lichens, bryophytes); (2) host nitrogen-fixing bacteria, providing major soil N input (lichens, bryophytes); (3) control soil chemistry and nutrition through the accumulation of recalcitrant polyphenols (bryophytes) and through their control over soil and vegetation hydrology and temperatures; (4) both promote erosion (rock weathering by lichens) and prevent it (biological crusts in deserts); (5) provide a staple food to mammals such as reindeer (lichens) and arthropodes, with important feedbacks to soils and biota; and (6) both facilitate and compete with vascular plants. Approach Here we review current knowledge about interspecific variation in cryptogam traits with respect to biogeochemical cycling and discuss to what extent traits and measuring protocols needed for bryophytes and lichens correspond with those applied to vascular plants. We also propose and discuss several new or recently introduced traits that may help us understand and predict the control of cryptogams over several aspects of the biogeochemistry of ecosystems. Conclusions Whilst many methodological challenges lie ahead, comparative cryptogam ecology has the potential to meet some of the important challenges of understanding and predicting the biogeochemical and climate consequences of large-scale environmental changes driving shifts in the cryptogam components of vegetation composition.