The study of asymmetry can provide insights into genetic and environmental influences on organismal development. Directional asymmetry (DA) can be either adaptive or non-adaptive, whereas fluctuating asymmetry (FA) – defined as small non-directional departures from symmetry in bilateral traits – is thought to be an indicator of genetic or environmental stress experienced during development. Using data from 28 European populations, we assessed the degree of DA and FA in the lateral plates of threespine sticklebacks Gasterosteus aculeatus and surveyed the direction of DA and differences in levels of DA and FA in different habitat types (viz. marine, lake and river populations). DA differed between habitats, with right-biased DA found in the marine populations and no directional bias found in lake and river populations. Differences in DA among habitats may be a by-product of habitat-specific developmental instability resulting in asymmetry, or it may indicate habitat-specific differences in selection against/for symmetry, as has been proposed in previous research of sticklebacks. Also, the presence of FA varied depending upon habitat type, but it also depended on plate morph – a variable confounded with the habitat effect. While we cannot rule out factors such as stress as a cause of population differences in FA, it may also simply be a by-product of other evolutionary processes (e.g. lateral plate number reduction) without functional basis.