It is widely accepted that the identification and management of abalone populations is critical for the ongoing sustainability of the fishery. However management of the endemic blacklip abalone throughout the Australian states generally occurs over large spatial scales and in some instances, across morphologically different populations on a finer scale. In this study, we use molecular techniques to show that blacklip abalone from seven sampling sites (of which four sites were characterized by stunted abalone growth patterns) in South Australia were genetically homogenous. Ten microsatellite loci and five composite restriction fragment length polymorphisms from the ND3/COIIImtDNA region showed high levels of genetic diversity across the collections, irrespective of growth characterization. Both molecular techniques also revealed a concordant outcome; no significant hierarchical variance was detected across geographically close, yet morphologically different collections (microsatellite φ;ST = 0.002; mtDNA φ;ST = -0.010). Pair-wise F_ST estimates were also low and often negative for the microsatellites (F_ST = -0.002 -0.007) and mtDNA markers (F_ST = -0.023-0.011). Our current findings support the hypothesis that blacklip abalone sampled here from “stunted” and “non-stunted” collections in the southern zone of the South Australian fishery are genetically similar.