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Due to the importance of camouflage to avoid detection by predators, predation pressure can cause coupled evolution of skin colour and preference for substrate colour. Individuals can choose regions where the background makes their skin colour less noticeable (crypsis) or where it accentuates warning coloration (aposematism). In such scenario, individuals should optimally choose substrate according to their skin colour and mechanism of predation avoidance: toxic species are expected to choose highly lit places and non-toxic species should avoid such places. We studied substrate choice on five species of tadpoles that differ in body colour and toxicity. The results of the present study did not confirm our prediction that non-toxic and cryptically coloured species would prefer a lower contrast substrate that maximizes camouflage. We show that individuals preferred highly lit areas that accentuated their contrast with the substrate. The general preference for lighter substrate might be related to the tadpole’s limited vision on a dark substrate, which hampers their ability in detecting predators. This study demonstrates that tadpoles can distinguish the substrate colour and that their choice of habitat might be linked to both their defence mechanism in the case of aposematic species and recognition of habitat elements in the case of cryptically-coloured species.