Colonies of the cosmopolitan urochordate Botryllus schlosseri that share one or both alleles at a single allorecognition locus (Fu/HC) and come into tissue contacts, may fuse and form a mixed entity, a chimera. Botryllus populations worldwide exhibit unprecedented extensive polymorphism at this locus, a result that restricts fusions to kin encounters. This study aims to compare spatiotemporal configurations in source and introduced B. schlosseri populations, residing on natural and man-made substrata, respectively. By using four microsatellite loci, we tested genetic consanguinity of colonies settled naturally along spatial vectors on both, natural (native populations) and man-made (introduced) substrates. Four populations were studied. Results revealed that B. schlosseri colonies, on both substrate types, assemble in groups of relatives that share similar microsatellite profiles. We suggest that this pattern of settlement promotes the formation of chimeras, which evoke conflicting interactions: cooperation between different somatic cell lines that constitute the colonial soma and competition between germ cells that inhabit the chimera gonads. Under natural conditions, the chimera may allow genetic flexibility that depends on joint genomic fitness of its partners. This is probably one of the life history characteristics that led to the worldwide distribution success of this species.