Spatial microbial ecology is an emerging new discipline in soil science and soil ecology which allows understanding not only the biogeography of soil organisms, but also the microbial regulation of organic matter cycling. Studies at the micro- and plot-scale will be presented: First, we will show studies using PLFA-SIP technique and qPCR analytics of functional genes elucidating bacterial and fungal specific use of substrates at the soil-litter interface. We revealed that a model compound (MCPA) was degraded either by bacterial metabolism or by fungal co-metabolism. Second, data from the Biodiversity Exploratories will show that microorganisms harbouring the same functional traits might either occupy similar or different niches at the plot scale. We could demonstrate that resource partitioning and transport of low molecular compounds are important mechanisms to shape the distribution, co-existence, and function of microorganisms in soils. Whereas governing factors responsible for the small-scale distribution and function of soil microorganisms are well understood, we are still lacking the most important biogeochemical properties ruling the plot-scale biogeography of soil microorganisms. .