The Peten was already the site of ceremonial architecture by the Maya civilization around 500 BC. El Mirador is the Peten's most important Pre-Classic Maya site. Later Peten became the heartland of the Maya Classic Period (c. 200 - 900). At it's height around 750 it is estimated that the Peten was home to several million people, being one of the most densely populated regions of the world at the time. Some areas are estimated to have had 2,600 people per square mile. Agriculture was very extensive, and there is some evidence suggesting that the land was depleted by unsustainable over-farming, resulting in a famine which was an important factor in the collapse of the Classic Maya states of this area. The population is estimated to have dropped by 2/3 between the mid 9th century and the mid 10th century.
After the Classic collapse the population of the area continued to drop massively. The first Europeans to visit the region, an expedition lead by Hernan Cortes which passed through in 1524 - 1525, reported that the region mostly had small hamlets separated by thick forest, with Tayasal being the only sizable inhabited city they observed in the region.
After Cortes' expedition, the Spanish largely left the Peten alone for generations until an expedition from Yucatán succeeded in conquering the last independent Maya state there in the late 17th century (see: Spanish conquest of Yucatán).
The Spanish town of Flores was established atop the site of Tayasal, but this remained an isolated backwater through the colonial era and after the independence of Mexico and Central America. When Guatemalan President Rafael Carrera sent a small force to Flores to claim the region for Guatemala in the 1840s, the governments of Mexico and Yucatán decided the region was not worth the trouble of contesting.
Starting in the 1960s the Guatemalan government offered land in Peten to any citizen willing to settle on it and pay a fee of $25. A road was opened up to Flores, although it was unpaved, and the notorious bus trip to Flores was known to take up to 24 hours to travel the 300 miles. Small airports were built at Flores and Tikal, bringing tourists to the region. In the early 1970s a road was opened from Tikal to Belize.
The first paved road in Peten was built in 1982.
Since the 1990s many new settlers have come to the Peten and it is experiencing severe deforestation.
El Peten consists of the following municipalites, listed with their population in 2000: