Accurate estimation of the impact of bottom fishing on vulnerable marine ecosystems (VMEs) requires knowledge of the distribution of those communities relative to the fishing footprint. If high target species catch rates are associated with habitats where VMEs are found, impacts from fishing would be higher than if VMEs are distributed randomly with respect to fishing locations. This study used the catch of the six most common vulnerable invertebrate taxa reported by observers on New Zealand vessels during the 2009/10 Ross Sea longline fisheries to correlate toothfish catch rates and benthic invertebrate catch rates at the scale of a longline segment, ~1 200 m. Analysis of the data available showed no evidence that the presence of any of six VME indicator taxa was informative in predicting Antarctic toothfish (Dissostichus mawsoni) catch at the scale of a longline segment. This supports conclusions of previous work finding no relationship between aggregate VME indicator taxa weight and toothfish catch at the scale of a longline set, ~7 km. Further studies at intermediate scales (10–100 km) would be useful to determine if both toothfish and individual VME indicator taxa have regionally concentrated distributions, showing a high degree of spatial overlap with the fishery.