With the upsurge in known membrane protein structures, common structural themes have started to emerge. One of these is the inverted repeat, a tandem of alpha-helical domains that have similar tertiary folds but opposite membrane orientations. In all previously known examples, both repeat units were encoded in a single continuous polypeptide. Recent structures of a bacterial multidrug transporter, EmrE, revealed an inverted repeat membrane protein wherein the two repeat units are assembled from two polypeptides with the same primary sequence. Here, we speculate on some of the implications of the EmrE structure with regards to our understanding of membrane protein evolution and topogenesis.