The spoon-billed sandpiper Calidris pygmaea is a Critically Endangered shorebird that breeds in the Russian arctic and winters in coastal and estuarine habitats in South-east Asia. We report the first formal estimate of its global population size, combining a mark–resighting estimate of the number of leg-flagged individuals alive in autumn 2014 with an estimate of the proportion of birds with flags from scan surveys conducted during the same period at a migration stop-over site on the Jiangsu coast of China. We estimate that the world breeding population of spoon-billed sandpipers in 2014 was 210–228 pairs and the post-breeding population of all age classes combined was 661–718 individuals. This and related methods have considerable potential for surveillance of the population size of other globally threatened species, especially widely dispersed long-distance migrants.