Morphometric variation was used to examine the stock structure, in southern Australian waters, of the deepwater marine teleost Hoplostethus atlanticus, orange roughy. Seven samples were collected from non-spawning aggregations in 1989–1990. Three samples were also collected in the winter of 1992, two from the main spawning site off the eastern coast of Tasmania (St Helens), and the third from the other main fishing ground south of Tasmania. The 38 morphometric measurements taken from each of over 1300 fish were size-standardized by an allometric formula and analysed by univariate and multivariate statistics. The results indicate significant variation in the morphology of orange roughy caught from geographically distinct aggregations. They further suggest that the main spawning aggregation may consist of fish from different groups at different times of the spawning period. There appear to be at least seven morphologically distinguishable stocks of orange roughy in southern Australian waters, despite genetic data indicating appreciable levels of gene flow between them.