The spatial distribution of potential interactants is critical to social evolution in all cooperative organisms. Yet the biogeography of microbial kin discrimination at the scales most relevant to social interactions is poorly understood. Here we resolve the microbiogeography of social identity and genetic relatedness in local populations of the model cooperative bacterium Myxococcus xanthus at small spatial scales across which the potential for dispersal is high. Using two criteria of relatedness - colony-merger compatibility during cooperative motility and DNA-sequence similarity at highly polymorphic loci - we find that relatedness decreases greatly with spatial distance even across the smallest scale transition. Both social and genetic relatedness are maximal within individual fruiting bodies at the micrometer scale but are much lower already across adjacent fruiting bodies at the millimeter scale. Genetic relatedness was found to be yet lower among centimeter-scale samples, whereas social-allotype relatedness decreased further only at the meter scale, at and beyond which the probability of social or genetic identity among randomly sampled isolates is effectively zero. Thus, in M. xanthus, high-relatedness patches form a rich mosaic of diverse social allotypes across fruiting-body neighborhoods at the millimeter scale and beyond. Individuals that migrate even short distances across adjacent groups will frequently encounter allotypic conspecifics and territorial kin discrimination may profoundly influence the spatial dynamics of local migration. Finally, we also found that the phylogenetic scope of intra-specific biogeographic analysis can affect the detection of spatial structure, as some patterns evident in clade-specific analysis were masked by simultaneous analysis of all strains. This article is protected by copyright. All rights reserved.