Intraspecific variability in social organization is common, yet the underlying causes are rarely known [1][2][3] . In the fire ant Solenopsis invicta, the existence of two divergent forms of social organization is under the control of a single Mendelian genomic element marked by two variants of an odorant-binding protein gene [4][5][6][7][8] . Here we characterize the genomic region responsible for this important social polymorphism, and show that it is part of a pair of heteromorphic chromosomes that have many of the key properties of sex chromosomes. The two variants, hereafter referred to as the social B and social b (SB and Sb) chromosomes, are characterized by a large region of approximately 13 megabases (55% of the chromosome) in which recombination is completely suppressed between SB and Sb. Recombination seems to occur normally between the SB chromosomes but not between Sb chromosomes because Sb/Sb individuals are non-viable. Genomic comparisons revealed limited differentiation between SB and Sb, and the vast majority of the 616 genes identified in the non-recombining region are present in the two variants. The lack of recombination over more than half of the two heteromorphic social chromosomes can be explained by at least one large inversion of around 9 megabases, and this absence of recombination has led to the accumulation of deleterious mutations, including repetitive elements in the non-recombining region of Sb compared with the homologous region of SB. Importantly, most of the genes with demonstrated expression differences between individuals of the two social forms reside in the non-recombining region. These findings highlight how genomic rearrangements can maintain divergent adaptive social phenotypes involving many genes acting together by locally limiting recombination.The fire ant S. invicta is characterized by a remarkable form of social polymorphism under the control of a single Mendelian factor [4][5][6]8 . Remarkably, a genomic element marked by the gene Gp-9 determines whether workers tolerate a single fertile queen (monogyne social form) or several fertile queens (polygyne social form) in their colony. Colonies containing only homozygous Gp-9BB workers accept only a single Gp-9BB queen, whereas colonies containing both Gp-9BB and Gp-9Bb workers will invariably accept several queens, but only Gp-9Bb queens 7,8 . The monogyne and polygyne social forms differ in numerous important aspects of their biology, including the level of aggression between colonies and how new colonies are initiated 9 . These important behavioural differences are associated with a suite of morphological and life-history differences among individuals with alternative Gp-9 genotypes, including queen fecundity, their tendency to accumulate fat during sexual maturation, the odour of mature queens, the number of sperm produced by males, and the size of workers [4][5][6][7][10][11][12] . The fact that Gp-9 codes for an odorant-binding protein (OBP), coupled with evidence that selection acted to drive the molecular diverg...