The Natural Temperate Grassland of the Victorian Volcanic Plain currently occupies less than 1% of its prior range prior. Consequently, many of the plant species endemic to the Volcanic Plain are in decline due to habitat loss. The hexaploid Senecio macrocarpus F. Muell. ex Belcher (Asteraceae), a perennial forb, is no exception and has been part of grassland reestablishment efforts in Victoria, Australia. In order to inform conservation efforts for S. macrocarpus, the population structure of S. macrocarpus was investigated with thirteen neutral microsatellite markers and maternal lineages (haplotypes) were identified from two chloroplast regions, psbJ-petA and trnL-rpL32. Senecio squarrosus is an uncommon species similar to S. macrocarpus,which occupies the same geographical area. This co-occurring hexaploid species was included in the study to elucidate any potential gene flow between the two species. A total of 529 S. macrocarpus and 28 S. squarrosus individuals over 20 populations were sampled. Genotyping identified a total of 104 multi locus genotypes from 557 total individuals. The most common clone was found 108 times across 10 different populations. Global F_st could not be estimated due to extreme variation between loci, either having a severe excess or deficit of heterozygosity. F_st within loci was estimated between 0.08 – 0.49.  Both PCoA and individual assignment results indicate that S. macrocarpus maintains the highest level of genetic diversity in the largest population located in South Australia. All other populations show similarity to the South Australian population via genetic distance and individual assignment of genetic clusters. Neutral markers show some S. macrocarpus individuals are nearly identical to the S. squarrosus individuals. Indicating recent speciation and common parent lineages. Chloroplast markers revealed few differences between populations of S. macrocarpus but were further removed from S. squarrosus individuals. The results suggest that S. macrocarpus may reproduce mainly via apomixis and this is the first evidence that supports apomixis in the tribe Senecioneae. This is being investigated further as apomixis within S. macrocarpus complicates the long-term viability and conservation of the species.