A genomic library was constructed and 14 novel polymorphic di- and tri-nucleotide nuclear microsatellite markers were developed for Melaleuca nematophylla, the Wiry Honey Myrtle, a common shrub of southwest Western Australia. Populations are patchily distributed in a highly fragmented landscape due to extensive vegetation clearing for agriculture and population genetic structure is being investigated to inform appropriate seed collection and restoration strategies. Moderate diversity was observed in two populations with the number of alleles per locus ranging from 2 to 17. Expected and observed heterozygosity averaged 0.606 and 0.423, respectively. All loci showed independent inheritance but there was evidence of possible null alleles at some loci in each population. © 2014 @Crown copyright as represented by the state of Western Australia.