The Dujo de Santa Fe is another valuable piece of the collection of the museum. The dujo is the symbolic seat of stone or wood used by the caciques (chiefs) and behíques (sorcerers) of the Taino society. The behiques, spiritual guides of the aboriginal peoples of the Caribbean, used the dujo to perform the ritual of the cohoba. During this ritual, with the help of the inhaled powders, consisting of tobacco leaf dust mixed with hallucinogenic plants, and great mental concentration, they could evoke the supernatural and could communicate with gods. The seat was well carved and polished in a design that allowed the behíque to rest on it, concentrating on his trip to other dimensions. On the other hand, these chairs were offered to important visitors to pay tribute. According the chronicles of Don Bartolome de las Casas, Christopher Columbus was hosted in the same way. 

The aboriginal ceremonial seat in the museum is carved from a single piece of guayacán wood that can be found at the mouth of the Santa Ana river in Santa Fe, west of Havana. It is very well carved and polished.  It is of 6th century. It represents a four-legged animal, with short legs and a small face. The slightly curved and raised tail forms the long support for back, so that the forward projected cemí (the animal figure) remains in between the legs of the resting person.

There is another dujo among the collection of the museum, the Dujo de Jauco. It was used as a ceremony tray for ceremonial offerings. It is carved from a single piece of guayacán wood. It was found in the cave at Mesa del Sordo, Jauco, close to Maisi in Baracoa. It is of the 7th century.

Yucahú Bagua Maórocote is supreme being in the Antillean mythology, particularly in the Aruacan mythology. It has not any ancestor, but a mother, Atabey. It is the invincible protector of man. It is the lord of the yucca and the sea. It is usually seen in three-tipped artifacts, carved from stones, called trigonoliths, that look like human body, frog, flamingo or manatee. Usually, these artifacts had a face with an open mouth, symbolizing the greed for ingesting nutrients from the soil. During the ritual, referring to Yúcahu Bagua Maórocoti, the trigonolith was buried into the soil next to the seed of the yucca and the Taino people were urinating on the seed to invoke Yucahuaguamá, the Yucca Lord, because it had the magical influence to fertilize the soil and to promote the harvest generously.

There are two guayos (graters) in the museum. The guayo is used to grate yucca and guáyiga to obtain the white dough of the cassava bread. The wooden one is from the 7th century and it was found in Baracoa. The other guayo is from Haiti and made of volcanic stone.

The collection contains also some plates, made of guayacán wood, and some vessels, made of caguairán root (a Cuban tree, characterized by its hard and resistant wood), that served to preserve or to carry food, particularly the cooked food.

A part of the pre-hispanic collection of the museum was acquired from the collection of the engineer Ernesto Segeth in 1934. It consists of petaloid axes, made of diorite and serpentine, and a stone mortar.

The sixth section of the museum is dedicated to the examples of the Mesoamerican and South American archeology. You can see the 6th century pan with zoomorphic handle from Central America, the stone statue of Aztec culture, representing the assistant of the priest carrying casserole for offering and the stone statues of two Aztec supernatural beings. One of the statues belongs to Chicomecoatl, the Aztec goddess of agriculture. While she symbolizes the agricultural prosperity, she was also called as Seven Serpent, as she was blamed for the years of poor harvest. The second statue belongs to the Feathered Serpent (Quetzalcoatl), the supernatural being, can be found in many Mesoamerican religions. Its feathered characteristics refers to its ability to fly, whereas as a serpent it represents its human nature to creep on the ground among other animals of the Earth.