Living in a social group can be both beneficial and costly for individuals, sometimes leading to social dominance and even lethal fighting. The desert seed-harvester ant Messor pergandei has long been used as a model system to study the adaptive value and dynamics of cooperation among queens during colony foundation. Previous studies in central Arizona suggested that young queens from cooperatively founded (pleometrotic) colonies always become aggressive soon after the colony is established, ultimately reducing to a single surviving queen. However, queens sampled from western Arizona and eastern California are significantly smaller in size, form much larger founding groups, and fail to show aggression in laboratory colonies, which together suggest that the queen aggression originally described may not occur in all pleometrotic populations. We tested whether multiple queens were retained past colony initiation in a western Arizona population by using microsatellites to determine if male and worker nest-mate genotypes were consistent with a single or multiple queens. Our analysis suggests that fatal queen fighting does not always occur, but rather pleometrotic queens from this area appear to coexist peacefully, sharing the colony and reproductive resources, a condition known as primary polygyny. The existence of geographic variation in aggressiveness among co-founding queens following worker emergence provides a unique comparative system to study the costs and benefits of social aggression.