The history of the discovery and exploration of the site is told through the accounts of various travelers who visited it from the 19th century onward, including Guillermo Dupaix, J.B. Carriedo, Johann von Müller, Désiré Charnay, and A.F. Bandelier, among others.

The Zapotec people flourished in the Central Valleys of Oaxaca, with archaeological evidence suggesting their origins date back around 2,500 years.

This area showcases Stelae 12 and 13, examples of the earliest known Zapotec writing. Two display cases are also present: the first shows the Zapotec ceramic sequence established by Alfonso Caso, while the second presents early figurines and urns found in residential areas of Monte Albán.

One of the most important sections is dedicated to Zapotec Writing, with 32 stelae carved with a variety of glyphs. This collection traces the evolution of their writing system, from simple symbols to more complex structures likely inspired by astronomical observation.

Here, visitors can see effigy vessels, figurines, and whistles found throughout the site, along with sculptures, ceramics, and mica of Teotihuacan style, demonstrating the strong trade and cultural exchange with the City of the Gods during Phase IIIB-IV.

This section includes three display cases:

Around the year 500 CE (Phase IIIA or early IIIB-IV), the Zapotecs extracted large greenstone slabs (volcanic tuff, or "cantera") from quarries in the valley—possibly from Ixcotel near Oaxaca City or the Etla Valley—and brought them up to Monte Albán.