The distribution of microscopic organisms (that is, those smaller than 2 mm) has been historically considered non relevant for biogeography, because of the idea that due to their small size, dispersal abilities, resting stages and quick reproductive rates, the presence of microscopic organisms in any place was not limited by geographical barriers and distances. Recent studies challenge this idea, and provide theoretical and empirical evidence in support of the existence of spatial patterns at different scales, and of biogeographical processes affecting many groups of microscopic organisms. Here we review the current state of the art for microbial biogeography, summarising sources of problems and misconceptions, but also their solutions advancing the general understanding of biogeography, and conclude suggesting new avenues for future research.