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Threespine stickleback exhibit a row of superficial neuromasts that project through the bony plates on each side of the trunk and which constitute an important sensory modality for detection of near-field water motion. Previously, we have shown that numbers of neuromasts on each structural plate are highly variable among populations. In the current paper, we expand this study to evaluate the extent of deviation from bilateral symmetry of 4344 fish in 57 natural and three transplant populations of threespine stickleback from lakes, streams and oceanic habitats of coastal British Columbia, predicting that neuromasts would be largely bilaterally symmetrical for optimal detection of external stimuli. In contrast, we found asymmetry in all populations, the greatest amount occurring on the anterior buttressing lateral plates and on populations with the fewest neuromasts. We found no consistent trends of signed (directional) asymmetry (SA) among the populations while relative absolute asymmetry (RAA) is lower in dystrophic (stained) habitats than in clearwater habitats (p < 0.001), except for fish with few neuromasts. Sexual dimorphism in RAA is also greater in dystrophic habitats (p < 0.001). Transplants from stained lakes to unstained ponds resulted in a 0.1% to 14% difference in RAA from the source population in less than 12 generations but varied in direction among experiments. Our data suggest a widespread tendency for populations exposed to reduced photic information to exhibit reduced asymmetry in their lateral line system, which can change rapidly in response to a new environment. [ABSTRACT FROM AUTHOR]