Sixteen polymorphic microsatellite loci were developed using a 454 sequencing approach, and three loci, developed for Sminthopsis douglasi, were optimized for the endangered sandhill dunnart, Sminthopsis psammophila. Nineteen loci (16 S. psammophila and three S. douglasi) were tested on 38 individual S. psammophila from two populations in South Australia. Three loci deviated from Hardy-Weinberg equilibrium, possibly due to null alleles. No evidence of linkage disequilibrium was detected. We recommend a final panel of 17 loci for future genetic analyses of S. psammophila, which will aid in conservation management of this poorly understood and nationally endangered marsupial.