For a long time Egyptologists believed that Meritaten must have married her father. Now, with smenkhare recognized as a real, male heir to the throne, it seems clear that she married her half-brother as he became co-regent to his father Akhenaten. The Amarna tomb of Meryre II provides us with a glimpse of the new royal couple. On the south and east walls of the main chamber we see Akhenaten, Nefertiti and their daughters; these walls were clearly carved before death tore the original Amarna family apart. The unfinished image on the north wall shows a king and queen standing beneath the rays of the Aten. The figures of the royal couple look like Akhenaten and Nefertiti but their recorded cartouches belong to 'King of Upper and Lower Egypt, Ankhkeprure son of Re, Smenkhkare' and the 'King's Great Wife Meritaten'. Unfortunately the king's cartouche has since been hacked off the wall by theives and is now lost.
Two unexplained princesses, Meritaten the Younger and Ankhesenpaaten the Younger, who appear at this time may well be daughters born to Meritaten and Smenkhkare (alternatively, they may be daughters born to Kiya and Akhenaten). But when Smenkhkare died after the briefest of reigns, most if not all of which had been spent ruling alongside his father Akhenaten, he left no male heir. After a possible brief and ill-documented period of rule by the otherwise unknown female king Neferneferuaten (Meritaten?), Smenkhkare was succeeded by his young brother Tutankhaten (re-named Tutankhamun) and his sister-consort, Ankhesenpaaten (Ankhesenamun). Meritaten, dis placed by her sister, vanished; her body has never been found.