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Abstract Background Altruism can be favored by high relatedness among interactants. We tested the effect of relatedness in experimental populations of the social amoeba Dictyostelium discoideum, where altruism occurs in a starvation-induced social stage when some amoebae die to form a stalk that lifts the fertile spores above the soil facilitating dispersal. The single cells that aggregate during the social stage can be genetically diverse, which can lead to conflict over spore and stalk allocation. We mixed eight genetically distinct wild isolates and maintained twelve replicated populations at a high and a low relatedness treatment. After one and ten social generations we assessed the strain composition of the populations. We expected that some strains would be out-competed in both treatments. In addition, we expected that low relatedness might allow the persistence of social cheaters as it provides opportunity to exploit other strains. Results We found that at high relatedness a single clone prevailed in all twelve populations. At low relatedness three clones predominated in all twelve populations. Interestingly, exploitation of some clones by others in the social stage did not explain the results. When we mixed each winner against the pool of five losers, the winner did not prevail in the spores because all contributed fairly to the stalk and spores. Furthermore, the dominant clone at high-relatedness was not cheated by the other two that persisted at low relatedness. A combination of high spore production and short unicellular stage most successfully explained the three successful clones at low relatedness, but not why one of them fared better at high relatedness. Differences in density did not account for the results, as the clones did not differ in vegetative growth rates nor did they change the growth rates over relevant densities. Conclusions These results suggest that social competition and something beyond solitary growth differences occurs during the vegetative stage when amoebae eat bacteria and divide by binary fission. The high degree of repeatability of our results indicates that these effects are strong and points to the importance of new approaches to studying interactions in D. discoideum.