If natural selection on fluctuating asymmetry (FA) is common and related to trait functionality, then vestigial traits should show elevated FA. Moreover, if FA increases with heterozygosity, then haploid males of haplodiploid taxa should exhibit higher PA than diploid females. We measured fluctuating asymmetry of functional traits (fore femora of soldier morphs and disperser morphs, and wings of dispersers) and a vestigial trait (wings of soldiers) in the eusocial haplodiploid gall thrips Oncothrips tepperi (Insecta: Thysanoptera). Wing FA, but not femur PA, was substantially and significantly higher in soldiers than in dispersers in both sexes. Patterns of intersexual variation in FA were complex: for wings, female soldiers had higher FA than male soldiers but male dispersers had higher FA than female dispersers, and for femora, males and females did not differ in FA in either morph. Our results suggest that vestigial traits exhibit higher FA because of relaxation of selection for functionality, and that haploidy does not necessarily lead to increased FA in males of haplodiploid taxa.