The Anasazi's Ancestors from 5,000 to 3,000 B.C.

The environmental period between 5,000 and 3,000 B.C. is often known as the Altithermal or Middle Holocene. Pollen studies indicate that an environment characterized by low moisture, hot temperatures, and overall instability. The analysis of organic remains in packrat middens reveals a climate in which the majority of rainfall occurs during the summer season, a shift from the earlier Pleistocene pattern of high winter precipitation. The effect of these changes on flora and fauna were quite dramatic. Woodlands retreated to higher and higher elevations, while desert scrub and grassland habitats expanded to the east and to the north. The conditions also caused almost all of the Pleistocene megafauna to become extinct, while other mammals, such as bison, retreated towards the Plains grasslands that remained to the east.

Middle Archaic people on the Colorado Plateau also responded to the marked environmental changes, especially during the Bajada Phase (4,800 to 3,300 B.C.), when the Altithermal was at its height. Archaeological remains indicate radical changes in settlement and subsistence patterns, and several scholars believe that many people began to move out of the region as they retreated to more mesic habitats. For example, evidence at both Sudden Shelter and Cowboy Cave indicate that they were abandoned. Dust Devil Cave, which during the Early Archaic had served as a base camp, became an overnight camp with ephemeral, featureless deposits. Archaic groups during this period continued to hunt, but due to the exodus of megafauna out of the Southwest, people had to rely on a wider variety of modern fauna. Plant resources also increased in importance as environmental changes led to the diversification of vegetation communities.

The design of Bajada Phase projectile points reflect a growing concern with conserving lithic material. Points became shorter and more finely made. Raw materials increasingly came from local sources of variable quality, which, along with a variety of new hafting techniques, contributed to an unprecedented diversity of projectile point designs. Meanwhile, expedient flake tools increased in use, as did large chopping tools, which may have been used to process coarse plant foods. Similarly, the appearance of the first groundstone artifacts reflects an increased reliance on plant foods.

While relatively little is known about Archaic groups on the Colorado Plateau, it is likely that they followed a pattern similar to that exhibited in the Mogollon highlands to the south. In this area, for example, Cordova and Bat Caves are situated on ecotones between the mountains and plains where people would have been able to access a broad spectrum of plants and animals. Deposits in these caves contain a diversity of wild plant remains, including pigweed, grasses, hackberry, goosefoot, walnut, juniper, prickly pear, Indian ricegrass, yucca, and numerous animal species. Recent studies also suggest that the occupants of these caves moved seasonally within a defined territory. For example, floral remains from Cordova Cave would have been available only during the late summer or early fall. The decrease in foreign lithic materials in sites that were earlier characterized by a greater diversity of local and non-local lithic materials also suggests a decrease in the range of Archaic groups, a restricted foraging pattern that was most likely conditioned by the availability and distribution of floral resources.