Several transitions to higher levels of biological organization have punctuated the history of life. These transitions occur when cooperative alliances lead to the integration of non-identical partners into more complex wholes. Yet there is inevitable conflict within these cooperative alliances. In the following chapters I investigate reproductive conflicts of interest between cooperators within insect societies and chimeric multicellular organisms. In the first chapter I show that in the tropical wasp, Parachartergus colobopterus, workers use aggression toward totipotent, emerging females to influence the reproductive future of the latter. By doing this workers resolve conflict over who reproduces in accord with their collective interests. In the second chapter I show that environmental heterogeneity can affect the outcome of conflict between co-aggregating clonal lineages of Dictyostelium discoideum. This helps account for the coexistence of cheaters and victims in natural populations of D. discoideum.