We tested whether some species are significantly linked to old calcareous fens at the millennial scale independent of the effect of recent fen area. We focused on vascular plants, bryophytes and land snails that differ in the degree of preservation of their remains in calcareous fen sediments and in their dispersal ability. Two land snail species, eleven vascular plant species and no bryophyte species have statistically significant affinities with old fens, independent of the effect of recent fen area. For one bryophyte and one snail, the effects of age and area are not distinguishable. The results for land snails, being abundantly preserved and easily determinable in calcareous fen deposits, are in full accordance with the direct macrofossil evidence. This suggests that our approach indirectly revealed a relict distribution of the species. Identification of species that are significantly linked to ancient localities at the millennial scale has great potential in palaeoecology and nature conservation.