The Commission aims to protect vulnerable marine ecosystems (VMEs) and has established several Conservation Measures that limit bottom fishing and require data collection by fishing vessels. Members have made substantive and important scientific contributions to support the Commission’s objective of protecting VMEs, but work comparing the effects of different gear types has been relatively limited. We used data collected by the longline fishery in Subarea 88.1 to compare the impacts of Autolines and Spanish longlines on VME taxa. We found that the probabilities of observing positive bycatches and the amounts of positive bycatch decreased with depth, but we also found that the rate at which positive bycatches decreased with depth was greater for Autolines than for Spanish longlines. Since we only analyzed data from areas where there was substantial spatial overlap of sets made with each gear type, we attributed the difference in rates at which positive bycatches decreased with depth to a difference in the rate at which VME taxa drop off Autolines relative to Spanish longlines while the gear is being hauled. We adjusted for this differential drop off to infer that Autolines have about 7 to 20 times greater impact on VME taxa per hook (or about 3.5 to 10 times greater impact per set). We believe that biased reporting (e.g., under-reporting by vessels using Spanish longlines) would change our specific findings but not our conclusion that Autolines have a substantially greater impact on VME taxa per unit fishing effort. Limiting the use of Autolines, which are in more intimate contact with the sea floor than Spanish longlines, may provide a precautionary approach to mitigating impacts on VMEs.