The diversity and species composition of the bryophyte flora colonizing the forest floor, live trees and deadwood in semi-natural broad-leaved forests of northern Germany was compared between a recent survey in 2013 and historical records from around 1900. The survey was based on the comparison of presence/absence data and their interpretation with help of ecological indicator values. Total species richness has declined in bryophytes growing on the forest floor but not in the other guilds, whereas a dramatic species turnover was found for all three guilds. This turnover was apparently primarily driven by the increased atmospheric load of reactive nitrogen from anthropogenic emissions. Sensitive species were replaced by more eutrophication-tolerant bryophytes; liverworts are overrepresented among the sensitive and thus declining species. Promotion of the competitive strength of vascular plants due to increased nitrogen levels is the likely cause of the reduction of bryophyte species richness on the forest floor. Former acidification by high atmospheric sulfur dioxide loads has left an imprint in the bryophyte vegetation by having favored acidophytic species and discriminating against basiphytic species. An increase in the mean indicator value for temperature suggests a beginning effect of climate warming on the bryophyte vegetation. Change in forest structure had an apparently smaller imprint on the bryophyte diversity of the studied semi-natural forests than atmospheric chemistry and climate. In this respect, bryophytes differ from the ecologically similar lichens, where published studies from the same region showed a dramatic decline of species richness and a stronger susceptibility to forest management.