The genetic basis for developmental stability, the ability of an organism to withstand genetic and environmental disturbance of development, is poorly understood. Fluctuating asymmetry (FA: small random deviations from symmetry in paired, bilateral traits) is the most widely used measure of developmental stability, and evidence suggests FA is weakly and negatively associated with genome‐wide heterozygosity. We investigated the genetic basis of developmental stability in the yellow dung fly. Fly lines were inbred for 16 generations at which time they were homozygous at the phosphoglucomutase (PGM) loci and PGM appears to influence FA in at least one other taxon. After 16 generations of inbreeding, lines homozygous for different PGM alleles were crossed and levels of FA for four metric traits were compared in the inbred and crossed flies. We also compared FA levels in these flies with previously gathered data on wild‐type (second generation outcrossed) flies, and additionally looked at the effects of two environmental stresses (larval food limitation and increased temperature) on FA. There were no significant differences in any measure of FA, nor in mean FA, in any trait when inbred and crossed flies were compared. Comparison of FA in these and wild flies also revealed no significant differences. Food limitation had no influence on FA, whereas heat stress increased FA of naturally, but not sexually, selected traits. Our results do not show a negative relationship between heterozygosity and FA, but support the notion that FA levels are stress, trait and taxon specific.