The parentage of Tutankhamun and Semenkhare is not critical to the conclusions summarized here, but does represent a most interesting mystery, and is one well worth outlining. (In addition to the discussion below, see Marshall ("Mark") Johnson's web site: http://www.axford.com/gb/unicorn/egypt/home.htm.)
A linen shirt of Tutankhamun found in his tomb dates Tutankhamun's birth to the seventh year of Akhenaten's reign (including coregency).(1) Osman believes that this shirt indicates that Tutankhamun was the son of Akhenaten, and that he was born between Akhenaten and Nefertiti's third and fourth daughters. Semenkhare, on the other hand, is described in inscriptions as "beloved" of Akhenaten, but is never referred to as his son. Other evidence, including Semenkhare's age (he was born before Akhenaten became coregent and presumably before Akhenaten and Nefertiti were married) all but preclude a father-son relationship. Therefore, if Tutankhamun and Semenkhare were brothers, it is more probable that they were both the sons of Amenhotep III.(2)
In an inscription at the Temple of Sulb in Nubia, Tutankhamun does refer to Amenhotep III as his father.(3) However, Akhenaten's name was later proscribed in Egypt in the same manner that Akhenaten had earlier proscribed the name of Amun, therefore, it is possible that Tutankhamun was obliged to refer to Amenhotep III as his father in the general sense (i.e., as a forefather). In his tomb, Tutankhamun is described as the "eldest son of the Aten in Heaven," indicating that he may have indeed been Akhenaten's first born son. It could, however, just as easily indicate that he was simply the eldest (and only) surviving royal son of Amenhotep III after the death of Semenkhare and banishment of Akhenaten. "Eldest son" of the god was also the customary title of a ruling Pharaoh regardless of whether he had been the eldest son of his father or not.
The identity of the mother(s) of Tutankhamun and Semenkhare is equally intriguing. We do know that Amenhotep III and Tiye had a daughter Beketaten who was born just two years before Tutankhamun.(4) However, a scarab found at the Temple of Osiris at Abydos names the mother of Tutankhamun as Merit-ra.(5) Merit-ra had been the name of Thutmose III's Royal Wife. Tiye became Royal Wife in the same manner as Merit-ra,(6) and may have assumed her name as well.
Besides Tiye, Amenhotep III had numerous minor wives, not the least of which was Sitamun who may have been considered by many to have been the true heiress. Alternatively, Merit-ra could have been Merit-aten, the eldest daughter of Akhenaten. Merit-aten had been elevated to the position of Royal Wife some time after Semenkhare had been named as coregent, possibly by virtue of bearing Akhenaten a royal son.
The root merit, or mery, means "beloved" and is the source of the Biblical names Miriam (sister of Aaron) and Mary (the mother of Jesus). It was also used in descriptions of Nefertiti and may have been one of her royal epithets.(7) There is evidence that Tutankhamun lived with Nefertiti both before and after he became Pharaoh, supporting the theory that Akhenaten and Nefertiti were the parents. However, Tutankhamun may have lived with Nefertiti only after his own mother was no longer alive.(8) A final candidate suggested as Tutankhamun's mother was a minor wife of Akhenaten named Kiye(9) whose status had been elevated by the designation, "the King's Favorite."
An obvious factor ruling against Akhenaten and Nefertiti as parents is Akhenaten's marriage to his daughters. This probably would not have occurred if Semenkhare and/or Tutankhamun had been conceived through Nefertiti. However, considering the effects of the plague, it may be that Tutankhamun had been so seriously ill (cf. Isaiah Chapter 53) that he was not expected to live or to be capable of becoming Pharaoh, and so an additional son was required. A further indication that Akhenaten was not the father is the relatively few articles bearing his name, or the names of his wives Nefertiti and Kiye, that were found in the tomb.(10) Articles bearing the names of Amenhotep III and Tiye are more numerous. A few articles bearing the name of Merit-aten were also found in the tomb.