Mountain glaciers worldwide have undergone net recession over the past century in response to atmospheric warming(1), but the extent to which this warming reflects natural versus anthropogenic climate change remains uncertain(2,3). Between about 11,500 years ago and the nineteenth century, progressive atmospheric cooling over the European Alps induced glacier expansion(2,4-6), culminating with several large-scale advances during the seventeen to nineteenth centuries(3). However, it is unclear whether this glacier behaviour reflects global or a more regional forcing. Here we reconstruct glacier fluctuations in the Southern Alps of New Zealand for the past 11,000 years using Be-10 exposure ages. We use those fluctuations to estimate the associated temperature variations. On orbital to submillennial timescales, changes in glacier snowlines in New Zealand were linked to regional climate and oceanographic variability and were asynchronous with snowline variations in European glaciers. We attribute this asynchrony to the migration of the intertropical convergence zone. In light of this persistent asynchrony, we suggest that the net glacier recession and atmospheric warming in both regions over the past century is anomalous in the context of earlier Holocene variability and corresponds with anthropogenic emissions of greenhouse gases.