Many studies have characterized students' difficulties in understanding and reasoning about scientific mechanisms. Some of those studies have drawn implications on teaching mechanisms and how to guide students while reasoning mechanistically. In this theoretical article, I claim that one component that has not garnered much attention in the science education literature, unlike other components of mechanistic explanations, is the black box construct, that is, missing mechanistic parts within mechanistic explanations (explanatory black box). By reviewing the literature on mechanisms and mechanistic explanations in the philosophy of science and cognitive psychology, I argue that explanatory black boxes are an inherent part of mechanistic explanations and that their recognition is essential for learning mechanisms, scientific literacy, and understanding the nature of science. Examples from biology education are provided as a case of a complex multileveled scientific field. In the absence of a pedagogical approach for teaching explanatory black boxes, I turn to studies and frameworks from computer science education that may guide educators on how to begin discussing this construct in the science classroom.