Our research investigates the effects of genetic relatedness between mates and male size on female mate choice in the agile antechinus (Antechinus agilis). Females were provided with a simultaneous choice between one large and one small male, with a minimum 5 g (a??20 of male weight) difference between males, in specially designed mate-choice enclosures. Genetic relatedness between males and females was determined using highly polymorphic, species-specific, microsatellite markers. Male size did not influence mate choice, with approximately equal numbers of large and small males chosen. Females chose males that were more genetically dissimilar to themselves significantly more times and showed significantly more sexual and non-exploratory behaviours near the genetically dissimilar males. The results show that, when free female mate choice is possible, female agile antechinus choose males on the basis of genetic relatedness, rather than male size.