The basal fern genus Botrychium presents both taxonomic challenges and issues related to conserving rare species. To track how individuals may vary morphologically and to improve our understanding of the demographic dynamics of this genus, we tracked the presence, size, and shape of 818 Botrychium sensu stricto individuals distributed over 23 sites in the Upper Peninsula of Michigan from 2008 to 2010. This is the first study we know of that tracks morphological change in the genus. Around 45% of the total number of plants observed in 2008 appeared in 2009 and 2010. About 20% of the individuals that did not reappear in 2009 subsequently re-emerged in 2010, confirming vegetative dormancy. Taller plants were likelier to emerge in subsequent years. However, height was uncorrelated with age so younger plants were as likely as older plants to reappear. New recruitment in 2010 was ~5.5%. Plant size and morphology were generally stable within seasons but changed between years, complicating efforts to delineate confusing species like Botrychium matricariifolium (Döll) A. Braun ex W. D. J. Koch. Species identity and traits in the previous year often predicted morphology but not consistently across all years and traits. Habitat differences among sites did not strongly affect reappearance or morphological change. However, height, morphology, and emergence may respond to variation in rainfall, herbivory, and/or interactions with mycorrhizal fungi or surrounding plants among years. Future studies should strive to estimate recruitment and survival over many years in order to distinguish dormancy from mortality, estimate longevity, track demographic fluctuations, and estimate long-term population viability.