Using 454 pyrosequencing and genomic enrichment techniques we developed 12 polymorphic markers for the endangered megapode, the malleefowl (Leipoa ocellata). Pyrosequencing on a 454 instrument resulted in 65 536 reads, with 3469 containing microsatellite repeats. Of these, 232 contained unique flanking sequences and had more than 8 repeat motifs. We chose 13 loci based on reliability of amplification and, from these, 12 unlinked loci were selected for genotyping. In a single population (n = 19), the 12 markers were moderately polymorphic (number of alleles per locus range = 3–7) and showed moderate to high levels of heterozygosity (0.285–0.882). Nine microsatellite primer pairs developed from the brush turkey (Alectura lathami), the closest living relative of the malleefowl in the family, Megapodiidae, failed to reliably amplify malleefowl DNA.