Understanding if morphological differences between organisms that occupy different environments are associated to differences in functional performance can suggest a functional link between environmental and morphological variation. In this study we examined three components of the ecomorphological paradigm – morphology, locomotor performance and habitat use – using two syntopic wall lizards endemic to the Iberian Peninsula as a case study to establish whether morphological variation is associated with habitat use and determine the potential relevance of locomotor performance for such an association. Differences in habitat use between both lizards matched patterns of morphological variation. Indeed, individuals of Podarcis guadarramae lusitanicus, which are more flattened, used more rocky environments, whereas Podarcis bocagei, which have higher heads, used more vegetation than rocks. These patterns translated into a significant association between morphology and habitat use. Nevertheless, the two species were only differentiated in some of the functional traits quantified, and locomotor performance did not exhibit an association with morphological traits. Our results suggest that the link between morphology and habitat use is mediated by refuge use, rather than locomotor performance, in this system, and advise caution when extrapolating morphology-performance-environment associations across organisms. •Differences in habitat use between Podarcis guadarramae lusitanicus and Podarcis bocagei.•Significant association between morphology and habitat use.•No association between locomotor performance and morphology.•Link between morphology and habitat use apparently mediated by refuge use.