Approximately 90% of the volume of the Gulf of Mexico is contained in water deeper than 200 m, a region where the Deepwater Horizon (DWH) blowout had more impact on ecosystems than any previous oil spill. The remoteness and relative inaccessibility of the deep sea makes documenting even acute impacts to the animals that live in this realm difficult. This article reviews Natural Resource Damage Assessment studies and follow-up work funded as part of the Gulf of Mexico Research Initiative that targeted deepwater pelagic and benthic fauna. Oil was incorporated into the pelagic food web, and a reduction in planktonic grazers led to phytoplankton blooms. Fish larvae were killed, and a generation may have been lost. Cetaceans were killed, and many avoided the area of the spill. In the benthic realm, there was a large loss of diversity of soft-bottom infauna, which were still not recovering a year after the DWH oil spill. Colonial octocorals that are anchored to the hard seafloor and are especially vulnerable to anthropogenic impact, died as a result of being covered with flocculent material containing oil and dispersant. Soft- and hard-bottom effects of the oil spill were found as much as 14 km away from the DWH wellhead site. Deep-sea communities in the Gulf of Mexico are diverse, play critical roles in the food web and carbon cycling, affect productivity, are sensitive to perturbations, and are at risk to contaminant exposure; thus, it is important to understand the effects on these natural resources.