The 13th Dynasty starts with the death of Nefrusobek, the last member of the royal family of the 12th Dynasty, who ruled Egypt. The two first kings of the new dynasty were sons of Amenemhat IV, who, although he was not of royal birth, ruled between Amenemhat III and Nefrusobek.

According to the Turin Kingslist, Nefrusobek's successor was named Wegaf. A comparison of material and sources, however, has led researchers to believe that the Turin Kinglist may have been wrong at this point. Seal impressions bearing Wegaf's name appear to belong more to the middle of the dynasty rather than its beginning. Similarly, Sebekhotep Sekhemre Khutawi, whom the Turin Kinglist places in the middle of the 13th Dynasty, appears to belong to the start of the dynasty. The fact that Sebekhotep and Wegaf had very similar prenomens, may have led to the two of them being mixed up in the kingslist.

Placing Sebekhotep Sekhemre Khutawi at the start of the dynasty, makes him the first king with the name Sebekhotep.

There are indications that already during the reign of Amenemhat IV, a local ruler in the Nile Delta of foreign origin became more and more powerful. It is during this reign that the frequent expeditions to the Sinai came to a stop, probably because the expeditions had to go via the Nile Delta. At the latest during the reign of Nefrusobek, this ruler was able to found his own dynasty, the 14th, which, ruling from the city of Avaris, controlled at least the eastern Nile Delta, and perhaps all of Lower Egypt.

Nefrusobek's successors of the 13th Dynasty thus only ruled over the Nile Valley, stretching from Memphis to Elephantine. The initial contacts between both rivalling houses may have been of a military nature, as the military burials of this period in Avaris seem to indicate. After these initial hostilities, a status quo appears to have been agreed and both houses coexisted peacefully, allowing each other access to their territories for trade.

The kings of this dynasty followed each other in rapid succession, hinting at a lack of stability of the central government which may have been caused by internal power struggles.

Very contrary to tradition that kingship was passed from father onto son, Sebekhotep III and several of his successors publically proclaimed being of non-royal birth, as if wanting to make a clear distinction between themselves and their predecessors. This too hints at the central government being plagued by power struggles.

There are also indications that towards the end of the 13th and 14th Dynasties, the fertile Nile Delta was ravaged by decades of famine. With more than 50% of the foodproduction of Ancient Egypt coming from this region, it is very likely that Upper Egypt, the realm of the 13th Dynasty, suffered as much.

Weakened by internal power struggles, famine and plagues that invariably accompanied longer periods of famine, the last kings of the 13th Dynasty were no match for a group of foreign invaders known as the Hyksos. Coming from Asia, the Hyksos had first overthrown the equally weak rulers of the 14th Dynasty and then pushed on further south, bringing the 13th Dynasty to an end.