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To understand how current patterns of habitat loss and fragmentation will ultimately affect ecosystem functioning, we need to match experimental manipulations of community structure with real changes occurring in the landscapes of today. In this study, we examine the consequences of habitat fragmentation on a key function: the decomposition of dung by invertebrates. In a microcosm experiment, we use previous observations of dung beetle assemblage structure in fragmented and intact landscapes to create realistic differences in assemblages of small, dung-dwelling species in the genus Aphodius. We ask whether such differences will affect ecosystem functioning, and how their effects compare to those of removing full functional groups: dung-dwelling Aphodius, tunnelling Geotrupes stercorarius, and/or earthworms. As measured by changes in dung fresh weight, we observe an overriding impact of removing G. stercorarius, with the amount of dung remaining at any one time doubling if the species is excluded. Compared to this major effect, there seem to be less effects of removing Aphodius, ambiguous effects of excluding earthworms, and no detectable effects of relatively minor changes in Aphodius assemblages as induced by current levels of fragmentation. Overall, our results support the general notion that different species contribute highly unevenly to overall ecosystem functioning. Most importantly though, our findings suggest that the functional consequences of habitat loss will depend on taxon-specific responses to landscape modification. Only by addressing these responses may we predict the actual consequences of habitat loss.