Several studies (e.g. Oke et al. 1997; Varela et al. 2012) have been conducted using distinct techniques (microsatellites,  allozyme or mtDNA analysis, diet and behaviour, etc.) in different geographic scales (New Zealand, Australia, Namibia, and Chile, North Atlantic). In samples collected from Hebrides (NW Ireland) to Sedlo bank (near the Azores archipelago), a panmitic population was found in the NE Atlantic and significant differences with the Namibian population (White et al. 2009). Genetic studies also found differences among New Zealand and Australian stocks (Branch 2001). But the worldwide stock structure of orange roughy is still currently unknown and a lack of significant differentiation among far geographic samples is revealed (Varela et al. 2012). Main fisheries are conducted in New Zealand, Australia, NE Atlantic and Namibia, where different regional units are considered for assessment and management purposes:

• Australia: four units are based on regional spawning grounds and migration patterns (Upston et al., 2014): Western Zone (Sandy Cape), Southern Zone (Maatsuyker and Pedra Branca), Southern Remote Zone (Cascade Plateau), Eastern Zone (St. Patricks Head and St. Helens Hill).
• New Zealand: presumable biological stock structure is based on the spawning grounds identified but the nine assessment/management units here considered according to main fisheries operating in the region, not always coincide with the boundaries of the biological stocks (more details in MPI, 2014a).
• Within the management unit Northern North Island (ORH 1) there are several biological stocks with unclear boundaries: Mercury-Colville is an assessment unit; there are other stocks that are not assessed
• Within the management unit Cape Runaway to Banks Peninsula (ORH 2A, 2B, 3A) there are two biological stocks and correspondent assessment units: East Cape (ORH 2A North) and Mid-East Coast (ORH 2A South, 2B, 3A)
• Within the management unit Chatham Rise and Puysegur (ORH 3B) there are at least two biological stocks with correspondent assessment units: NW Chatham Rise, East and South Rise, Puysegur and the remainder of the sub-Antarctic area
• Within the management unit Challenger Plateau (ORH 7A) there is a biological stock which includes also the Westpac Bank outside the New Zealand EEZ, managed by the South Pacific RFMO.
• West coast South Island (ORH 7B)
• In the NE Atlantic there are 3 units recognized but considered as inadequate according to the species’ biology and sparse information available (ICES 2008, OSPAR Commission 2010): Rockall, NW Scotland and North Ireland (Subarea VI), Irish Sea, SW Ireland, Porcupine Bank, English Channel and Bristol Channel, Celtic Sea (Subarea VII) and NE Atlantic includes remaining areas (areas I, II, IIIa, IV, V, VIII, IX, X, XII, XIV). 
• Off Namibia according to the last stock assessment report (South East Atlantic Fisheries Organization 2014;Bensch et al. 2009).