Ecological interactions are the glue of biodiversity, structuring communities and determining their functionality. However, our knowledge about ecological interactions is usually biased against cryptic interactions (i.e. overlooked interactions involving inconspicuous species). Mosses are a neglected component in community ecology despite being diverse and abundant in boreal and temperate forests. Therefore, the cryptic relationships of trees as hosts for epiphytic mosses, and vertebrates using mosses as nesting material, may have important consequences for community structuring. We built species- and individual-based ecological networks to characterise tree–moss associations in 120 tree individuals representing 13 species, which hosted 19 moss species. We also used those ecological networks to simulate the effects of non-random extinctions due to selective logging, to assess the presence of moss species in hummingbird nests (30 nests), whether these mosses were a subset of those found on the trees if moss diversity varies with tree height and whether these moss–tree relationships are phylogenetically constrained. We found a nested pattern in the tree–moss network. Taller trees were the most connected, with tree height positively related to number of moss species, network degree and centrality. Extinction simulations showed changes in network topology, with the strongest effect from the removal of the most connected tree species. However, tree and moss networks were not influenced by phylogenetic relatedness. The hummingbird Sephanoides sephaniodes selectively collected mosses; the moss species used as nesting material by hummingbirds were a subset of available species. These complex relationships among trees, birds and mosses underpin the importance of neglected components in the community. We found that tree–moss associations were non-random, showing a positive relationship between tree height and moss diversity. Those associations are the reflection of preferences beyond relative abundances in the forest, and the removal of certain tree species (due to selective logging) may have cascade effects in the community. Furthermore, the lack of phylogenetic correspondence suggests that tree–moss associations are governed by ecological factors (host tree preferences). Moss–hummingbird associations are non-random, as hummingbirds (that pollinate these trees) are actively selecting mosses for nest building, stressing the importance of cryptic interactions as a community-structuring process. A free Plain Language Summary can be found within the Supporting Information of this article.