Nine polymorphic microsatellite markers were developed for a nationally endangered marsupial, the southern brown bandicoot (Isoodon obesulus) using a next generation sequencing approach. The nine markers were genotyped in 59 individuals from two distinct locations (the Mt Burr Range and the Mt Lofty Ranges) in South Australia. All loci showed Hardy-Weinberg equilibrium with the exception of one locus in the Mt Lofty population, possibly because of null alleles. No evidence of linkage disequilibrium was detected. These markers will provide valuable resources for future projects on the conservation genetics of southern brown bandicoots in Australia.