The applicability of fluctuating asymmetry (FA) in conservation biology as a bio-marker and an early warning system have been examined in various groups of animals. However, cave-dwelling invertebrates have gotten little attention and yet caves have no biological management. Thus, developing a bio-marker to identify early responses of cave-dwelling species to stress provides a valuable tool to account for in future conservation and management programs. We examined whether FA can be used as a bio-marker of relaxed selection for cave-dwelling invertebrates. Specifically, we compared FA levels of pedipalps and two segments of chelicerae (chelicel1 and chelicel2) between cave and surface habitats and among populations in a troglophilic harvestman specie, Paranemastoma sillii sillii (Herman, 1871). Under the assumption that cave environment exerts relaxed selection we hypothesised that cave-dwelling harvestmen express higher degree of FA than surface-dwelling harvestmen. Because female and male harvestmen use the pediplaps differently, we assumed sex-specific selective pressures and further examined the effect of sex and habitat (cave vs surface) and sex interaction on FA levels. We hypothesised no differences in the levels of FA among harvestman cave populations, because of the idea that relaxed selection is responsible for higher levels of FA in cave-dwelling harvestmen rather than environmental stress. We found significant habitat sex interactions in the FA of the pedipalp. Interactions of population and sex had a significant effect on pedipalp and chelicel2 FA. These results partially support the idea that FA responds to differences in the strength of selection. Although we cannot fully disentangle the mechanisms of natural selection affecting FA and the study of trait asymmetry should be combined with studies of other sources of stress (i.e. genetic stress, predation, prey availability) we conclude that FA could be a bioindicator to be used as a tool in conservation and management of cave.