The following pages contend that, in spite of its intensive development, contemporary cognitive science has recently entered a phase of fairly acute uncertainty and confusion regarding some of its most essential foundations. They emphasize two aspects of this foundational crisis, specifically vindicating the existence of a crisis of naturalism and of a crisis of representationalism. Like any foundational crisis, this situation constitutes a serious threat to the significance of the empirical achievements of cognitive science. A threat calling for renewed efforts to provide it with secure foundations that can only be obtained through acloser collaboration between empirical and foundational investigations, or, more concretely, between cognitive scientists and philosophers. They also outline a general strategy to address this threat, and illustrate itabout one aspect of particular importance of the naturalist crisis, namely the emergentist challenge to the orthodoxy of non reductive functionalism. They argue for the rejection of one version of this emergentist challenge,and they lay out a minimal condition that any other version of emergentism must meet. It is still unclear whether this condition is yet satisfactorily met by some version, and in particular by the sort of emergentism associated with the notion of dynamical system. Clarifyingthis issue should accordingly be seen as a top priority on the agenda of cognitive philosophy.