Sekhemre Khutawy Sobekhotep is usually considered Dynasty XIII's first pharaoh, and Merneferre Ay, while not the final pharaoh, was the last to occupy the Middle Kingdom capital of Itjtawy, and the last of the dynasty with a significant recorded reign.

However, the period may have been more peaceful than was once thought since the central government in Itj-tawy near the Faiyum was sustained during most of the dynasty and the country remained relatively stable.

The period was undoubtedly characterized by decline, with a large number of kings with short reigns and only a few attestations.

[9] Daphna Ben Tor believes that this event was triggered by the invasion of the eastern Delta and the Memphite region by Canaanite rulers.

According to Manetho, into this unstable mix came invaders from the east called the Hyksos who seized Egypt "without striking a blow; and having overpowered the rulers of the land, they then burned our cities ruthlessly, razed to the ground the temples of gods..." Their regime, called Dynasty XV, was claimed to have replaced Dynasties XIII and XIV in most of the country.

In a recently published paper in Egypt and the Levant,[11] Nadine Moeller, Gregory Marouard and N. Ayers discuss the discovery of an important early 12th dynasty Middle Kingdom administrative building in the eastern Tell Edfu area of Upper Egypt which was in continual use into the early Second Intermediate Period until the 17th dynasty, when its remains were sealed up by a large silo court.

However, this analysis and the conclusions drawn from it are rejected by Egyptologist Robert Porter, who argues that Khyan ruled much later than Sobekhotep IV (a gap of c. 100 years exists between the two in conventional chronologies) and that the seals of a pharaoh were used long after his death.

[13] Merneferre Ay was the last Egyptian ruler of the 13th Dynasty who is attested by objects in both Lower and Upper Egypt.