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Theoretical efforts and small‐scale experiments have given rise to the widespread belief that the fewer occurrences a species has or the more fragmented its distribution is, the more vulnerable that species should be to extinction. Lacking, however, are large‐scale multi‐species studies exploring the connection between rarity and local extinction risk. Here we present a landscape‐level biogeographic test of this widely assumed linkage. Using a unique data set detailing the occurrence patterns of freshwater fishes of the Sonoran Desert (a gravely endangered fauna) we obtained for each of 25 species a measure of rarity that was independent of spatial scale. We found that fragmentation was consistently associated with elevated extinction risk, whereas the number of occurrences exerted a significant effect only if fragmentation had not already been accounted for. Specifically, desert fish species with the most …