This dataset was collected on the cruise JC136 in May and June 2016. This cruise is associated with a NERC joint standard research grant (NE/K011855/1 and NE/K013513/1) entitled “Influence of population connectivity on depth-dependent diversity of deep-sea marine benthic biota”. The aims of the project are to investigate connectivity among deep-sea populations at different depths and spatial scales using: 1) larval dispersal modelling using Lagrangian particle tracking, driven by hydrographic models, 2) population genetics/genomics, and 3) benthic community analysis. The aims of cruise JC136 were then to sample a range of sites and depth bands to: 1. obtain physical samples of 4 model organisms for molecular analysis, 2. gather benthic biological survey data for community level analysis, 3. collect oceanographic data to validate high-resolution oceanographic models with which we will model larval dispersal. The chief scientists of this cruise were Kerry Howell (University of Plymouth School of Marine Science and Engineering) and Michelle L Taylor (University of Oxford Department of Zoology). This dataset contains a variety of navigation data (position, heading, bathymetry), atmospheric measurements (air temperature, wind speed and direction, irradiance and humidity) and sea surface hydrographic data (transmittance, chlorophyll fluorescence, sea surface temperature and conductivity). Data were collected in the NE Atlantic (Rockall Bank, George Bligh Bank, Anton Dohrn Seamount, Wyville-Thomson Ridge, Rosemary Bank) from 27 ROV dives, 12 AUV missions, 43 CTD casts, 2 mooring deployments and equipment trials. All cruise aims were broadly met. 3630 biological samples were obtained, including sufficient depth and site coverage for molecular analysis of 3 target species. Video transect data was also obtained, with sufficient replication and depth stratification from 3 sites and near complete sampling from a 4th. This cruise provides sufficient oceanographic data to validate our models. In addition, 5811.66 km2 of seafloor multibeam was collected to contribute to ongoing efforts to map the North Atlantic, including the first multibeam from the Geike Slide and Hebridean Slope Nature Conservation Marine Protected Area (NCMPA). Poor visibility at the seabed prevented a planned resurvey of the Darwin Mounds Marine Protected Area (MPA).