
Archaeological sites in Colombia are numerous and diverse, including findings and archaeological excavations that have taken place in the area now covered by the Republic of Colombia. The archaeological finds and features cover all periods since the paleolithic, representing different aspects of the various cultures of ancient precolumbian civilizations, such as the Muisca, Quimbaya and Tairona among many others. Preservation and investigation of these sites are controlled mainly by the Ministry of Culture, the National Institute of Anthropology and History, and the Bank of the Republic. The lack of funding to protect sites and enforce existing laws, results in large scale looting and illegal trading of artifacts.

El Abra is the name given to an extensive archeological site, located in the valley of the same name. El Abra is situated in the east of the municipality Zipaquirá extending to the westernmost part of Tocancipá in the department of Cundinamarca, Colombia. The several hundred metres long series of rock shelters is in the north of the Bogotá savanna on the Altiplano Cundiboyacense, Eastern Ranges of the Colombian Andes at an altitude of 2,570 metres (8,430 ft). The rock shelter and cave system is one of the first evidences of human settlement in the Americas, dated at 12,400 ± 160 years BP. The site was used by the hunter-gatherers of the Late Pleistocene epoch.

Aguazuque is a pre-Columbian archaeological site located in the western part of the municipality Soacha, close to the municipalities Mosquera and San Antonio del Tequendama in Cundinamarca, Colombia. It exists of evidences of human settlement of hunter-gatherers and in the ultimate phase primitive farmers. The site is situated on the Bogotá savanna, the relatively flat highland of the Altiplano Cundiboyacense close to the present-day course of the Bogotá River at an altitude of 2,600 metres (8,500 ft) above sea level. Aguazuque is just north of another Andean preceramic archaeological site; the rock shelter Tequendama and a few kilometres south of Lake Herrera. The artefacts found mostly belong to the preceramic period, and have been dated to 5025 to 2725 BP. Thus, the younger finds also pertain to the later ceramic Herrera Period. There were some difficulties in dating of the uppermost layer due to modern agricultural activity in the area; the sediments of the shallower parts were disturbed.

The Archaeology Museum of Pasca is an archaeological museum located in Pasca, Colombia. It houses a great collection of Pre-Columbian objects and human remains, including Muisca mummies. It has a replica of the famous golden raft, Balsa Muisca, found near this town that represents the El Dorado rite. The museum hosts a piece of Muisca textile from Belén, Boyacá. The total collection numbers 2500 pieces. Apart from the Muisca artifacts, the museum hosts material from the Tairona, Calima, Quimbaya, Sinú, San Agustín and Tierradentro, among others.

Checua is a preceramic open area archaeological site in Nemocón, Cundinamarca, Colombia. The site is located 7 kilometres (4.3 mi) north of the town centre. At Checua, thousands of stone and bone tools, stone flakes and human remains have been found, indicating human occupation from around 8500 to 3000 years BP.

Ciudad Perdida is the archaeological site of an ancient city in Colombia's Sierra Nevada de Santa Marta. It is believed to have been founded about 800 CE, some 650 years earlier than Machu Picchu. This location is also known as "Teyuna" and "Buritaca 200".
The Cojines del Zaque is an archeological site of the Muisca located in the city of Tunja, Boyacá, which in the time of the Muisca Confederation was called Hunza. The cojines are two round stones used in the religion of the Muisca to worship Sun god Sué and his wife; Moon goddess Chía. When the Spanish conquistadores arrived, they called them Cojines del Diablo.

El Morro del Tulcán is an Indigenous pyramid in Popayán, Colombia. Research suggests that the individuals buried there came from the very top of the social classes of their society.

The Goranchacha Temple is an archeological site of the Muisca located in the city of Tunja, Boyacá, which in the time of the Muisca Confederation was called Hunza. The temple is named after the mythological Goranchacha. The remains of the temple are located on the terrain of the Pedagogical and Technological University of Colombia in Tunja. Scholar Javier Ocampo López has written about the temple and its religious meaning. Knowledge about the temple has been provided by chronicler Pedro Simón.

The Hunzahúa Well is an archeological site of the Muisca located in the city of Tunja, Boyacá, which in the time of the Muisca Confederation was called Hunza. The well is named after the first zaque of Hunza; Hunzahúa. The Well was called Pozo de Donato for a while, after 17th century Jerónimo Donato de Rojas. The well is located on the terrain of the Pedagogical and Technological University of Colombia in Tunja. Scholar Javier Ocampo López has written about the Well and its mythology. Knowledge about the well has been provided by scholar Pedro Simón.

El Infiernito, is a pre-Columbian archaeoastronomical site located on the Altiplano Cundiboyacense in the outskirts of Villa de Leyva, Boyacá, Colombia. It is composed of several earthworks surrounding a setting of menhirs ; several burial mounds are also present. The site was a center of religious ceremonies and spiritual purification rites, and also served as an astronomical observatory.

Lake Herrera is a small lake located at 5 kilometres (3.1 mi) from the urban centre of Mosquera and about 20 kilometres (12 mi) west of the capital Bogotá in Cundinamarca, Colombia. The Andean lake has made its name in the Herrera Period, the period in the history of central Colombia before the Muisca Period, after archaeologist Sylvia Broadbent excavated ceramics around Lake Herrera in 1971.

Malagana, also known as the Malagana Treasure is an archaeological site of Colombia named after the same name sugarcane estate where it was accidentally discovered in 1992. During a few days after its discovery, the place was subject to a large scale looting with a rough estimated of 4 tons of pre-Columbian artifacts illegally removed from the burial mounds. A rescue archaeological mission was sent by the National Institute of Anthropology and History (ICANH), led by archaeologist Marianne Cardale de Schrimpff. Archaeological excavations at the site established a previously unknown cultural complex, designated as Malagana-Sonsoid, that dates between 300 BC to 300 AD
Piedras del Tunjo is an important archaeological park established on a natural rock shelter 40 kilometres (25 mi) west of Bogotá in the municipality of Facatativá.

The San Agustín Archaeological Park is a large archaeological area located near the town of San Agustín in Huila Department in Colombia. The park contains the largest collection of religious monuments and megalithic sculptures in Latin America and is considered the world's largest necropolis. Belonging to San Agustin culture, it was declared a UNESCO World Heritage Site in 1995. The dates of the statues are uncertain, but they are believed to have been carved between 5–400 AD. The origin of the carvers remains a mystery, as the site is largely unexcavated.

San Agustín is a town and municipality in the southern Colombian Department of Huila. The town is located 227 km away from the capital of the Department, Neiva. Population is around 34,000. The village was founded in 1752 by Alejo Astudillo but attacks by indigenous people destroyed it. The present village was founded in 1790 by Lucas de Herazo and Mendigaña.

Tequendama is a preceramic and ceramic archaeological site located southeast of Soacha, Cundinamarca, Colombia, a couple of kilometers east of Tequendama Falls. It consists of multiple evidences of late Pleistocene to middle Holocene population of the Bogotá savanna, the high plateau in the Colombian Andes. Tequendama was inhabited from around 11,000 years BP, and continuing into the prehistorical, Herrera and Muisca periods, making it the oldest site of Colombia, together with El Abra, located north of Zipaquirá. Younger evidences also from the Herrera Period have been found close to the site of Tequendama in Soacha, at the construction site of a new electrical plant. They are dated at around 900 BCE to 900 AD.

Tibitó is the second-oldest dated archaeological site on the Altiplano Cundiboyacense, Colombia. The rock shelter is located in the municipality Tocancipá, Cundinamarca, Colombia, in the northern part of the Bogotá savanna. At Tibitó, bone and stone tools and carbon have been found. Bones from Haplomastodon, Cuvieronius, Cerdocyon and white tailed deer from the deepest human trace containing layer of the site is carbon dated to be 11,740 ± 110 years old. The oldest dated sediments are lacustrine clays from an ancient Pleistocene lake.

Tierradentro is one of the ancient Pre-Columbian cultures of Colombia. It started to flourish around 200 BC, and continued into the 17th century.