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Extinction-risk assessments aim to identify biological diversity features threatened with extinction. Although largely developed at the species level, these assessments have recently been applied at the ecosystem level. In South Africa, national legislation provides for the listing and protection of threatened ecosystems. We assessed how land-cover mapping and the detail of ecosystem classification affected the results of risk assessments that were based on extent of habitat loss. We tested 3 ecosystem classifications and 4 land-cover data sets of the Little Karoo region, South Africa. Degraded land (in particular, overgrazed areas) was successfully mapped in just one of the land-cover data sets. From <3% to 25% of the Little Karoo was classified as threatened, depending on the land-cover data set and ecosystem classification applied. The full suite of threatened ecosystems on a fine-scale map was never completely represented within the spatial boundaries of a coarse-scale map of threatened ecosystems. Our assessments highlight the importance of land-degradation mapping for the listing of threatened ecosystems. On the basis of our results, we recommend that when budgets are constrained priority be given to generating more-detailed land-cover data sets rather than more-detailed ecosystem classifications for the assessment of threatened ecosystems., (© 2013 Society for Conservation Biology.)