This study presents a new approach to examining European chiton habitat use according to morphological characteristics. Time-search transects were conducted on four Portuguese rocky shores at two shore levels. The chiton species, abundance and individual morphometric features were recorded and related to the substratum dominant epiphytes and surface roughness. The chiton Lepidochitona cinerea (Linnaeus 1767) was the dominant species (77%), followed by Leptochiton algesirensis (Capellini 1859) (15%) and Acanthochitona crinita (Pennant 1777) (8%). Species abundance did not vary significantly with shore level or amongst shores. Six colour morphs were considered for Lepidochitona cinerea, four for A. crinita and one for Lepidochiton algesirensis. Substratum characteristics significantly explained the variation in species and colour morph distribution. There was a high correlation between the presence/absence and type of epiphytic algae and the substratum surface roughness level. We hypothesize that three mechanisms operating either independently or in interaction may explain the non-random distribution of colour polymorphisms according to their habitat characteristics: (i) presence of algae that are part of their diet; (ii) use of rock as shelter – for instance, crevices and cover resulting from algae fronds and; (iii) morph–rock colour matching as a camouflage mechanism to reduce predation pressure.