Aim This study aims to evaluate the role of various factors in structuring biogeographical distribution of small‐sized organisms. More specifically, we analysed the distribution of three groups of marine benthic organisms differing in body size, both unicellular and metazoans, to assess the relevance of geographical and environmental factors on their taxonomic composition. Location Global. Taxon Heterotrophic flagellates, Ciliophora, Harpacticoida (Copepoda). Methods The set of predictors included species richness (a proxy for sampling effort), geographical distance, isolation by geographical or hydrological barriers and three environmental variables (sea surface temperature, its annual variation and salinity). Multiple regression on the distance matrices and null modelling were used to quantify the relative effects of these variables in taxonomic similarity among 21 regions of the Ocean. Results Each group showed a unique biogeographical pattern. The smallest‐sized organisms, the flagellates, had high regional but low global diversity and low endemicity and demonstrated worldwide, environmentally driven distribution without any dispersal limitation (only the effects of climatic variables, but neither distance nor isolation effects, were significant). Thus, flagellates basically meet the ‘ubiquity model’ of global distribution. The ciliates showed a moderate level of endemicity, and their distribution depended on both spatial distance and the climatic variables, in accord with the ‘moderate endemicity model’. In contrast, harpacticoids demonstrated high endemicity level, and their distribution was mostly geographically driven, indicating the considerable role of dispersal limitation—the pattern typical of other multicellular taxa with ‘classical biogeography’. Species richness significantly influenced the interregional similarity of each group and explained 26%–65% of the total variance, indicating the strong impact of undersampling on faunistic similarity estimations. Main conclusions Our results support the hypothesis that body size is the ‘master trait’ that shapes global biogeographical patterns towards higher predictability and increasing role of dispersal limitation for larger organisms.