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One of the key goals of conservation biology is to determine what causes declines in biodiversity and suggest ways of stopping or slowing them down. Studies on the temporal changes in the distributions of species provide critical information on temporal trends in local extinctions and information on what causes these changes. This is especially true for endangered groups of plants, such as orchids. Here we analysed changes in the distributions of orchids in the Czech Republic over three time periods when the agricultural practices differed. Orchids were divided into two groups based on whether they provide nectar to their pollinators. Moreover, we determined the effect of three different spatial resolutions on the interpretation of the results. Many species in the Czech orchid flora have become rarer over time and four became extinct. These changes are directly associated with changes in the agricultural practices in the Czech Republic that started in the 1950s, which especially resulted in the abandonment of traditional management. Mosaics of small fields were converted into huge fields and the application of artificial fertilizers increased dramatically, both of which resulted in loss of natural habitats and decline in many species of orchids - both nectariferous and nectarless species. Our results are important for conservation and are aimed at preventing further decline in orchid sites and recovery of orchid populations.