We isolated and characterized eight novel microsatellite loci in the southern emu-wren (Stipiturus malachurus). We used nonradioactive polymerase chain reaction (PCR)-based techniques to screen an enriched genomic DNA library. Based on genotypes from a single population, six loci showed no evidence of null alleles and were polymorphic (allele range = 2–9, mean heterozygosity = 0.57), and one locus was sex-linked (NA = 4). These loci were variable and had different allele size ranges in three other populations of southern emu-wrens, and are therefore useful for determining levels of genetic diversity within and between populations of the species.