Social interactions among microbes that engage in cooperative behaviors are well studied in laboratory contexts [1, 2], but little is known about the scales at which initially cooperative microbes diversify into socially conflicting genotypes in nature. The predatory soil bacterium Myxococcus xanthus responds to starvation by cooperatively forming multicellular fruiting bodies in which a portion of the population differentiates into stress-resistant spores [3, 4]. Natural M. xanthus populations are spatially structured [5], and genetically divergent isolates from distant origins exhibit striking developmental antagonisms that decrease spore production in chimeric fruiting bodies [6]. Here we show that genetically similar isolates of M. xanthus from a centimeter-scale population [7] also exhibit strong and pervasive antagonisms when mixed in development. Negative responses to chimerism were less intense on average among local strains than among global isolates, although no significant correlation was found between genetic distance at multilocus sequence typing (MLST) loci and the degree of social asymmetry between competitors. A test for self/nonself discrimination during vegetative swarming revealed a great diversity of distinct self-recognition types even among identical MLST genotypes. Such nonself exclusion may serve to direct the benefits of cooperation to close kin within diverse populations in which the probability of social conflict among neighbors is high.