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Global biodiversity patterns are often driven by different environmental variables at different scales. However, it is still controversial whether there are general trends, whether similar processes are responsible for similar patterns, and/or whether confounding effects such as sampling bias can produce misleading results. Our aim is twofold: 1) assessing the global correlates of diversity in a group of microscopic animals little analysed so far, and 2) inferring the influence of sampling intensity on biodiversity analyses. As a case study, we choose rotifers, because of their high potential for dispersal across the globe. We assembled and analysed a new worldwide dataset of records of monogonont rotifers, a group of microscopic aquatic animals, from 1960 to 1992. Using spatially explicit models, we assessed whether the diversity patterns conformed to those commonly obtained for larger organisms, and whether they still held true after controlling for sampling intensity, variations in area, and spatial structure in the data. Our results are in part analogous to those commonly obtained for macroorganisms (habitat heterogeneity and precipitation emerge as the main global correlates), but show some divergence (potential absence of a latitudinal gradient and of a large-scale correlation with human population). Moreover, the effect of sampling effort is remarkable, accounting for >50% of the variability; this strong effect may mask other patterns such as latitudinal gradients. Our study points out that sampling bias should be carefully considered when drawing conclusions from large-scale analyses, and calls for further faunistic work on microorganisms in all regions of the world to better understand the generality of the processes driving global patterns in biodiversity.