Little is known about the pre-Hispanic Itza'. Legend has it that the Itza' migrated to Yucatán from elsewhere in Mexico or were a remnant Classic Petén Maya group that moved north to Yucatán. After competing with the Xiu clan for control of the Yucatán Peninsula, the Itza' settled in Petén, perhaps in the 1450s (however, some scholars believe they may have settled there around 1200). According to some interpretations of indigenous history recorded in colonial-era Yucatecan Mayan documents called Books of the Chilam Balam (derived from the name of the famous prophet— chilam —who was known as balam, jaguar), the Itza' fled the region of Chichén Itza' in northern Yucatán to found their island capital of Tayasal in Lake Petén Itza'. There they formed a confederacy composed of four loosely allied political groups. They resisted the Spanish until 1697, about a century and a half after most Mayan groups were conquered. The Itza' maintained contact with other Mayans in Yucatán and in Belize throughout the colonial period, and there probably were waves of migrants from the north who fled the Spanish to settle in Petén. They also had intermittent contact with the Mopan Maya in southern Petén, the Lakantun to the west, and Q'eqchi' immigrants from the Verapaces, Guatemala. Until the 1970s, large stands of tropical forest and the absence of good roads made travel to Petén difficult and helped maintain its relative isolation.
Hernán Cortés passed through the region in 1524 on his way from Mexico City to Honduras, where he planned to punish a subordinate lieutenant, Cristóbal de Olid. He reported being well received by the Itza' "king" Kanek' at Tayasal, present-day Flores. During the colonial era, the Itza' periodically received Spanish emissaries but steadfastly resisted conversion to Catholicism and submission to Spanish authority. Tayasal remained a center of Itza' culture, including the Mayan hieroglyphic scribal tradition, and also inspired Mayan resistance to Spanish domination in Yucatán and Belize, until it was conquered during a Spanish military campaign in March 1697. Warfare and European diseases decimated the Itza' population, which has remained small since the seventeenth century. Indians in the region were forced to live in mission towns or to flee into the forest. San José was one of these mission towns and the only one in which an Itza' ethnic identity has survived to the present.
After 1697, the Itza' of San José were primarily traditional swidden farmers cultivating staples—maize, beans and squash—as well as many supplemental crops. They sold surplus agricultural products as well as clay water jugs, canoes, firewood, construction materials, and other forest products. Since the Conquest, San José and all of Petén have been politically and economically dominated by a mixed Creole and Ladino elite residing in Flores.
In the 1890s, demand for chicle, a tree-resin base for chewing gum, transformed the regional economy of Petén. The chicle boom lasted until about 1970. During the chicle harvest season, from July to February, men formed base camps in the forests, from which they fanned out daily to tap chicle from sapodilla trees. Almost all Itza' men participated in the chicle harvest, as did many other Peteneros. Chicleros (chicle workers) and their families were dependent on a patron, who often supported them until the men returned home from the forest. Chicleros were renowned for pre- and postharvest extravagant and exuberant celebrations. Since the 1960s and 1970s, tourism and extraction of timber and other forest products have become primary industries in the region.
In the 1960s the Guatemalan government sponsored settlement of Petén and, in 1970, completed a road from the more densely populated highlands. Since then, large numbers of immigrants have come to Petén. The Itza' have resisted allowing newcomers to settle in San José, forcing them to found new villages nearby.
In the 1980s the civil war in Guatemala affected Petén, where the military maintain a strong presence. Guerrilla groups have been active in Petén since the 1970s but decreasingly so since the peak of the violence in the mid-1980s. San José was was not occupied or attacked by either side; however, San Joseños, like other Peteneros, were terrified by the violence.
The interest in conservation and ecotourism has brought many foreigners to the region, and the Itza' have become involved in conservation efforts. They are in constant contact with outsiders but so far have generally succeeded in keeping them out of San José.