AimDespite growing knowledge on deep‐sea benthic fauna, patterns of changes in species composition combining both bathymetric and latitudinal variation are still poorly known. In the first synthesis on the beta diversity patterns of assemblages of hydroids across an entire ocean basin, our aim was to infer limits and gradients of species distribution along depth and latitude.LocationAtlantic Ocean and adjacent polar seas.TaxonHydrozoa.MethodsHydroids from 50 to 5,330 m deep were studied primarily based on museum collections. Identifications were made by the authors, improving uniformity within the dataset by avoiding variations in taxonomic interpretation. Data totalled 3,699 records belonging to 432 species, at 1,444 unique sites. Records were assigned to three depth strata (50–200, 201–1,000 and 1,001–5,330 m) and eight latitudinal bands of 20° each, totalling 24 sample areas. We conducted non‐metric multidimensional scaling (NMDS) ordination, clustering and PERMANOVA analyses of species compositions and abundances per area to examine differences and relationships in hydroid assemblages among areas.ResultsAssemblages primarily differentiate between those to the north and south of 40°S, regardless of depth, with southern ones separated between Patagonian and Antarctic. Northwards of 40°S, assemblages differentiate gradually along both depth and latitude, although a faunal turnover occurs at 1,000 m deep. Also, assemblages at 1,001–5,330 m deep tend to be more similar to each other than assemblages at shallower strata, suggesting significant connectivity over great distances in the deep sea. We note the problem of largely unequal hydroid sampling in the Atlantic Ocean across depths and latitudes, especially in the southern hemisphere and below 1,000 m deep.Main ConclusionsAssemblages of hydroids differentiate gradually along latitude and depth, with more rapid shifts in species composition occurring at 40°S, 60°S and at 1,000 m deep. Greater similarity was found among deeper water assemblages.