Here we report the development of 10 microsatellite loci for the alpine caddisfly, Allogamus uncatus. Polymorphism as detected in 24 individuals ranged from three to 17 alleles per locus, and observed heterozygosity ranged from 0.087 to 0.864. These primers will enable research on the genetic population structure of this species, the extent of gene flow among alpine permanent and temporary streams, and the genetic consequences of extinction/recolonization events. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.