Zieria obcordata A.Cunn. (Rutaceae), an endangered species endemic to central New South Wales, Australia, faces significant conservation challenges due to limited occurrence in two small, isolated populations. Using genome-wide SNPs (DArTseq), we examine genetic relationships and diversity within and between these populations, and make comparisons with other Zieria species. Our results confirm that Z. obcordata is a distinct species, with the Bathurst and Wellington populations showing sufficient genetic divergence to warrant recognition as two subspecies: Z. obcordata subsp. obcordata and Z. obcordata subsp. wuuluman (formally described here). Minor morphological differences further support this classification. Genomic analyses reveal minimal gene flow between the subspecies, along with extremely low heterozygosity and high inbreeding coefficients within each. Compared to other Zieria species, including Z. covenyi, Z. cytisoides, Z. laevigata, Z. odorifera and Z. smithii, both subspecies exhibit exceptionally low genetic diversity, likely due to geographic isolation, genetic drift and inbreeding. We provide conservation assessments for both subspecies and conclude that each qualifies to be listed as Critically Endangered under the New South Wales Biodiversity Conservation Act 2016. We recommend strategies to facilitate gene flow between the subspecies to improve genetic diversity and enhance fitness.