Greater Rheas (Rhea americana) have a social mating system in which several females lay eggs in communal nests, and males incubate and care for chicks. Behavioural observation methods used so far are insufficient to unravel if females form a cohesive “harem,” simultaneous polyandry (promiscuity) occurs in the wild, and multipaternity occurs in each clutch. We used molecular markers to conduct for the first time a genotype-based sibship and parentage assignment analysis among reproductive individuals and their offspring, within and between nests, in a wild Greater Rhea population of central Argentina. In a 4800-ha area, we found five nests from which we collected complete clutches and feathers of incubating males. We successfully determined the genotypes of three males and all 141 offspring at 8 microsatellite loci. We inferred the parents involved in matings and their genotypes based on offspring’s genotypes. A total of 37 males and 47 females were engaged in the assigned pairings, and one incubating male did not fertilise any egg. We obtained three main novel results that enlighten the mating system of Rheas: (a) females do not form “harems”; (b) there is evidence of promiscuity; and (c) incubator male does not father the majority of offspring from his nest. The strategy of Greater Rheas is to copulate with several individuals simultaneously and lay eggs in different nests, independently of whether or not the incubating male fathers those eggs. These results provide a new and significant step in understanding the complex mating system of this ratite.