The association between lateral‐line canals and skull bones in fishes has been the subject of several studies and raised a series of controversies, particularly with regard to the hypothesized role of lateral‐line organs (i.e. neuromasts) in osteogenesis and the consequences for hypotheses of homology of the bones associated with lateral‐line canals. Polypteridae, a group of freshwater fishes that occupies a key phylogenetic position as the most basal extant lineage of ray‐finned fishes (Actinopterygii), provides an interesting model for the study of the relationships between lateral‐line canals and skull bones. We describe the development of bones associated with lateral‐line canals in the Senegal Bichir, Polypterus senegalus, and use these data to re‐address previous hypotheses of homology of skull bones of polypterids. We demonstrate that the lateral‐line canals constitute a separate component of the dermatocranium that may interact with a membranodermal component, thereby forming compound bones in the adult. Differences in the interactions between these components determine the characteristics of the development of each independent bone in the skull of adult P. senegalus. Our results shed light on long‐standing controversies about the identity of skull bones such as the rostral, preopercle, and sphenotic in Polypteridae, and suggest the presence of an ancestral two‐component pattern of formation of bones associated with lateral‐line canals in bony fishes. These findings reveal the need to re‐address previous hypotheses of homology of bones associated with lateral‐line canals in different groups of bony fishes, especially fossil taxa.