Premise of the study: Recent habitat fragmentation is posing a risk to the wavy-leaved smokebush, Conospermum undulatum, a rare plant species endemic to the south-western Western Australia. Microsatellites markers are required to characterize the genetic diversity and structure of the species for conservation purposes and to facilitate ecological studies. Methods and Results: Illumina MiSeq high-throughput sequencing was used to develop 20 novel microsatellite markers for C. undulatum. Polymorphism at each locus was assessed using 72 individuals from three natural populations. Nineteen markers were polymorphic, with the number of alleles per locus ranging from two to 21, and observed and expected heterozygosity ranging from 0.000 to 1.000 and 0.117 to 0.919, respectively. All markers successfully amplified in three congeneric species. Conclusions: The microsatellite markers will be useful for revealing patterns of genetic diversity, dispersal dynamics and hybridization events for C. undulatum to inform future conservation efforts.