The history of psychology has been marked by strong methodological, theoretical and epistemological controversies. In this paper, we evaluate the hypothesis that these well-known controversies are often implicitly supported by philosophical, metaphysical and probably religious oppositions. The focus of our investigation concerns the classical opposition in philosophy between dualism and physicalism, more specifically the complex relationship between the brain and the mind. One hundred and sixty-six teachers and researchers (30 in clinical psychology, 37 in cognitive psychology, 31 in development psychology, 38 in social psychology and 30 in neurosciences) from 8 French universities have accepted to participate in this survey by responding to a questionnaire made of 17 questions. Data were analyzed using factor analysis technique and the results of the principal component analysis (PCA) revealed four main factors that are more likely to define accurately the philosophical profile of each sub-discipline. The main result of this survey is that philosophical and metaphysical positions, at the foundations of psychology, clearly distinguish and oppose the five studied sub-disciplines. At one extreme, there are cognitive psychologists and neuroscientists who are strongly physicalist. To the contrary, clinical and social psychologists exhibit more dualistic representation. Developmental psychologists occupy an intermediate position between these two extremes. Finally, we analyzed the implications of the participants’ philosophical representation differences, from an epistemological and clinical/practical point of view. The important point is that these philosophical and metaphysical oppositions are largely implicit. Indeed, inside our community, it is very rare, if not exceptional, that they are explicitly involved in the theoretical or epistemological conflicts, which exist inside our discipline. However, it is probable that they play a massive role in our debates, a role all the more important, as we are largely unconscious of them. The current study is the first to tackle such an important topic by describing more accurately the philosophical representation of scholars in major sub-fields of psychology. By revealing such deep metaphysical oppositions, we hope to shed a new light on the origins of these persisting conflicts in psychology.