Knowledge of the distribution of rare species is crucial for species conservation in fragmented habitats. Species communities often exhibit nestedness, i.e. species in species-poor sites comprise a subset of richer ones. Thus, rare species are confined to species-rich sites. We evaluate whether plant and fungal communities in 46 old-growth spruce forest patches (0.17–12 ha) exhibit nestedness. The question whether a single large patch or several small patches capture most species (i.e. the SLOSS-issue) is evaluated in combination with species saturation analyses. All species groups exhibited significant nestedness. Area was generally related to nestedness, i.e. rare species were over-represented in the largest patches. Species saturation analysis indicated that large patches accumulated more Red-list species in patch interiors than small patches. Thus, rare and Red-list species were best captured in large patches. However, nestedness also emerged in equal sized sample plots, i.e. rare species were over-represented in high quality habitats. Thus, small habitats of high quality should not be neglected in a conservation perspective.