The frequency of extra-pair paternity (EPP) among birds varies considerably, with the highest rates (56–76%) reported in several species of fairy-wren (Maluridae). According to the ‘constrained female’ hypothesis, such high frequencies arise when females are emancipated from constraints on mate choice because they have access to alternative sources of parental care (cooperative breeding). We investigated the genetic mating system of a close relative of the fairy-wrens within the Maluridae, the southern emu-wren (Stipiturus malachurus). Southern emu-wrens share several life-history attributes with the fairy-wrens, but show relatively low levels of cooperation, providing an opportunity to assess how the frequency of cooperative breeding correlates with the frequency of EPP. We assessed paternity for 50 offspring within 27 emu-wren broods using species-specific microsatellite markers. Overall, only 12% of genotyped offspring resulted from extra-pair paternity, and 15% of broods contained at least one extra-pair offspring. We argue that opportunities for mate choice by female emu-wrens are restricted by their dependence on paternal care for offspring survival, as suggested by the constrained female hypothesis. The low occurrence of cooperative breeding in the southern emu-wren may thus help explain the extreme variation in the frequency of extra-pair paternity within this family.