Eight novel microsatellites were isolated and characterised in the thorn-tailed rayadito Aphrastura spinicauda in order to evaluate genetic diversity in three contrasting populations, two of them at the boundaries of the geographic range of the species. All loci were found to be polymorphic and 3–15 alleles were found per locus. Expected and observed heterozygosity ranged from 0.26 to 0.89 and from 0.27 to 0.87, respectively. Global and pairwise Weir and Cockerham's Fst showed that genetic differentiation was greater between the northern population and the ones in central and southern Chile. The eight markers developed will be useful to study the genetic diversity of the thorn-tailed rayadito across its distribution.