Although intraspecific variability is now widely recognized as affecting evolutionary and ecological processes, our knowledge on the importance of intraspecific variability within invasive species is still limited. This is despite the fact that quantifying the extent of within-population morphological divergences associated with the use of different trophic or spatial resources (i.e. resource polymorphism) can help to better predict their ecological impacts on recipient ecosystems. Here, we quantified the extent of resource polymorphism within populations of a highly invasive species, Procambarus clarkii, in 16 lake populations by comparing their trophic (estimated using stable isotope analyses) and morphological characteristics between individuals from the littoral and pelagic habitats. Our results first demonstrated that crayfish occur in both littoral and pelagic habitats of 7 lakes and that the use of pelagic habitat was associated with increased abundance of crayfish in the littoral habitat. We then found that individuals from littoral and pelagic habitats displayed significantly different body and chelae morphology and origin of resource use (i.e. reliance on littoral carbon). These results demonstrate the existence of resource polymorphism in invasive populations. There was no genetic differentiation between individuals from the two habitats, implying that this resource polymorphism was stable (i.e. high gene flow between individuals). Finally, we demonstrated that a divergent adaptive process was responsible for the morphological divergence in body and chela shapes btween habitats while difference in origin of the resource use neutrally evolved under genetic drift. These findings demonstrated that invasive P. clarkii can display strong within-population phenotypic variability in recent populations, and this could lead to contrasted ecological impacts between littoral and pelagic individuals.