Spatial datasets and associated metadata to support the publication of 'An atlas of seabed biodiversity for Aotearoa New Zealand'. The atlas contains prediction of spatial distribution, with associated uncertainty, of over 600 seafloor associated taxa throughout New Zealand waters and were developed using species distribution modelling approaches. Metadata containing model evaluation, expert appraisal scores and ancillary information for all spatial layers in the 'An atlas of seabed biodiversity for Aotearoa New Zealand' is also provided. A manuscript, accompanying the publication of the atlas, has been submitted under the same title. The abstract for the manuscript is as follows. The waters of Aotearoa New Zealand span over 4.2 million km2 of the South Pacific Ocean and harbour a rich diversity of seafloor associated taxa. Due to the immensity and remoteness of the area, there are significant gaps in the availability of data to quantify and map the distribution of seafloor and demersal biodiversity, limiting effective management. In this study, we describe the development and accessibility of an online atlas of seabed biodiversity that aims to fill these gaps. Species distribution models were developed for 579 taxa across four taxonomic groups: demersal fish, reef fish, subtidal invertebrates and macroalgae. Spatial layers for taxa distribution based on habitat suitability were statistically validated and then, as a further check, evaluated by taxonomic experts to provide measures of confidence to guide the future use of these layers. Spatially explicit uncertainty (SD) layers were also developed for each taxon distribution. We generated layer-specific metadata, including statistical and expert evaluation scores, which were uploaded alongside the accompanying spatial layers to an online open access marine data portal hosted by the New Zealand Department of Conservation. The online atlas is fully interactive, with search and plotting functions, and allows the export of single or multiple spatial layers on seafloor biodiversity. The atlas provides the most comprehensive database on the distribution of seafloor taxa for Aotearoa New Zealand and is thus an invaluable resource for managers, researchers and the general public that will guide the management and conservation of seafloor communities.