Documenting phenotypic variation among populations is crucial for our understanding of micro-evolutionary processes. To date, the quantification of trophic and morphological variation among populations of coral reef fish at multiple geographical scales remains limited. This study aimed to quantify diet and body shape variation among four populations of the damselfish Dascyllus abudafur living in different environmental conditions from the central Red Sea and from Madagascar. Stomach content analyses showed that one adaptive response of D. abudafur inhabiting turbid waters is a trophic shift from almost exclusive zooplanktivory to a diet consisting of planktonic and benthic prey. Our morphometric data reveal differences in cephalic profile and body shape among populations, in agreement with this variation in trophic strategy. Isotopic diversity and body shape disparity vary among populations and we thus demonstrate that coral reef fish populations are not equal in terms of phenotypic diversity among sites and regions. Finally, our comparative analysis reveals that the main axes of body shape variation among populations are shared at both small (Red Sea sites) and large (Madagascar and Red Sea sites) spatial scales. This study raises new questions about the factors governing the direction of response to selection in this fish species.