Impacts of Patagonian toothfish bottom-set longline fishing on vulnerable marine ecosystems (VMEs) are examined in a licenced fishery and adjacent areas beyond national jurisdiction (ABNJ) lacking fishery management. VME taxa distributions were predicted using MaxEnt and compared to fishing footprints of ABNJ and licenced fleets. The ABNJ fishery footprint was almost twice as large as in licenced waters. Whilst the footprint of low fishing effort (0.0–3.4 h km−2) was similar between areas, footprints of medium (3.4–10.2 h km−2) and high (10.2–45.3 h km−2) fishing effort were 4 and 13 times greater, respectively, in ABNJ. Percent overlap of licenced fishing distribution on VME indicator taxa groups was low (6.45–9.82%) compared to the considerably higher (32.62–61.99%) percentage fishing overlap on VME indicator distribution in ABNJ. Our results show that, despite the main area of VME indicator taxa being found within jurisdictional waters, there are important VME habitats on the adjacent high-seas that are potentially highly impacted by unregulated fishing. This raises concerns regarding the potential for ABNJ fisheries to undermine domestic VME management where VMEs straddle managed areas and areas that are inconsistently managed or unmanaged. Management of VMEs would benefit from strengthening regional high-seas fishing governance and monitoring procedures.