SUMMARY Drosophila melanogaster has long played an important role in debates surrounding insect and arthropod head segmentation. It is surprising, therefore, that one important feature of Drosophila head segmentation has remained controversial: namely the position of the boundary between the intercalary and mandibular segments. The Drosophila embryonic head has a pair of structures lying behind the stomodeum known as the hypopharyngeal lobes. Traditionally they have been seen as part of the intercalary segment. More recent work looking at the position of the lobes relative to various marker genes has been somewhat equivocal: segment polarity gene expression has been used to argue for a mandibular affinity of these lobes, while the expression of the anterior‐most hox gene labial (lab) has supported an intercalary affinity. We have addressed the question of the segmental affinity of the hypopharyngeal lobes by conducting a detailed comparison of gene expression patterns between Drosophila and the red flour beetle Tribolium castaneum, in which the intercalary segment is unambiguously marked out by lab. We demonstrate that there is a large degree of conservation in gene expression patterns between Drosophila and Tribolium, and this argues against an intercalary segment affinity for the hypopharyngeal lobes. The lobes appear to be largely mandibular in origin, although some gene expression attributed to them appears to be associated with the stomodeum. We propose that the difficulties in interpreting the Drosophila head result from a topological shift in the Drosophila embryonic head, associated with the derived process of head involution.