The ability to identify and separately manage component populations is becoming increasingly important in guarding against overexploitation of many marine species. Blacklip abalone (Haliotis rubra) form isolated populations with variable life history characteristics as a result of the heterogenous areas they inhabit. Many of these populations are ‘stunted’, reaching a lower maximum size compared with those in adjacent areas. We obtained a range of morphological measurements from samples of ‘stunted’ and ‘non-stunted’ H. rubra collected from sites spread across broad (tens of kilometres) and fine (hundreds of metres) spatial scales in southern South Australia. The ratio between shell length and shell height showed clear and significant differences among samples from ‘stunted’ and ‘non-stunted’ sites. The morphometric collections from the sub-sites suggested that ‘stunted’ populations existed at smaller spatial scales (up to 400 m) compared with that for ‘non-stunted’ populations (at least 1000 m). The ‘morphometric marker’ developed in the present study has the potential to be used as a tool to identify individual populations rapidly and cost-effectively that can then be managed separately. Our approach is applicable to other species of abalone as well as other sedentary invertebrates with limited larval dispersal.