Genetically similar cells of the soil bacterium Myxococcus xanthus cooperate at multiple social behaviours, including motility and multicellular development. Another social interaction in this species is outer-membrane exchange (OME), a behaviour of unknown primary benefit in which cells displaying closely related variants of the outer-membrane protein TraA transiently fuse and exchange membrane contents. Functionally incompatible TraA variants do not mediate OME, which led to the proposal that TraA incompatibilities determine patterns of intercellular cooperation in nature, but how this might occur remains unclear. Using natural isolates from a centimetre-scale patch of soil, we analyse patterns of TraA diversity and ask whether relatedness at TraA is causally related to patterns of kin discrimination in the form of both colony-merger incompatibilities (CMIs) and inter-strain antagonisms. A large proportion of predicted TraA functional diversity documented among global isolates is contained within the cm-scale population. We find evidence of balancing selection on the PA14-portion of TraA and extensive transfer of traA alleles across genomic backgrounds. CMIs are shown to be common among strains identical at TraA, suggesting that CMI kin discrimination is not generally caused by TraA dissimilarity. Finally, it has been proposed that inter-strain antagonisms might be caused by OME-mediated toxin transfer. However, we find that most strain pairs exhibiting strong antagonisms are predicted to be incapable of OME due to TraA dissimilarity. Overall, our results suggest that documented patterns of kin discrimination in a defined natural population of M. xanthus are not causally related to the degree of TraA relatedness among interactants.