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Premise of the study: Microsatellite loci were developed for the ectomycorrhizal fungus <i>Laccaria</i> sp. A to investigate the population genetic structure of this fungal symbiont across its fragmented distribution in southeastern Australia. Methods and Results: A partial genome sequence from an individual collection of <i>Laccaria</i> sp. A was obtained by 454 genome sequencing. Eight microsatellite markers were selected from 66 loci identified in the genome. The selected markers were highly polymorphic (4–19 alleles per locus, average 13 alleles) and amplified reproducibly from collections made across the distribution of this species. Five of these markers also amplified reproducibly in the sister species <i>Laccaria</i> sp. E (1). All eight of the selected microsatellite loci were from the mitochondrial genome. Conclusions: The highly polymorphic markers described here will enable population structure of <i>Laccaria</i> sp. A to be determined, contributing to research on mycorrhizal fungi from a novel distribution.