This funerary basilica was located next to the Roman road connecting Mértola to Beja. This important monument was partially excavated in the late 19th century, and several funerary inscriptions were recovered from it, now housed in the National Archaeological Museum in Lisbon. Currently, it houses a museum where the foundations and floors of the former church are preserved. This museum contains inscribed stelae, which constitute the most important collection of Early Christian tombstones found in Portugal.

The Roman House was the first museum section of the Mértola Museum to open in 1989. It is located in the basement of the City Hall building. During renovation work, important archaeological remains corresponding to the foundations of a Roman house (today it serves as the main building) emerged. In addition to the walls of the old building, where part of the house's impluvium stands out, period architectural elements, funerary epigraphy, ceramics, and metalwork are on display. Each section has a permanent exhibition related to its theme.

The former Misericórdia Church of Mértola houses the first municipal museum of sacred art. This space, known as Porta da Ribeira, presents a unique collection of images and liturgical artefacts from hermitages and chapels of popular worship. Here, the different nuances of humanity's relationship with various references to the sacred are reconstructed, with the exhibition of sacred art from the 14th to 18th centuries, liturgical artefacts, including chalices and processional crosses, and painted tablets.

The Islamic Art Center opened in 2001 and represents the culmination of many years of work not only in archaeological interventions but also in the treatment and study of materials from the Islamic period. The collection, dating from the 9th to 13th centuries, comprises architectural elements, funerary epigraphy, ceramics, metals (copper and copper alloys, iron, and lead), worked bone (including artifacts directly related to weaving and glass objects).

A true live museum where the visitors may watch craftspeople working. It features the traditional "mantas" of Mértola.

The blacksmith's Forge, inaugurated in June 2001, corresponds to the musealization of an ancient workshop of farrier and blacksmith. It is a small workshop set up in the vicinity of one of the gates of the village. The forge ended its activity when its owner, died in the mid-eighties of the 20th century, and was subsequently acquired by the local authority. In this museum you can see a small part of the estate representative of this artisan activity.

The Museum of smuggling is a small museum structure you want, above all, to perpetuate the memory of the smuggling activity in this territory raiano. Installed in the former Fiscal guard post Santana de Cambas, intends to function as place of registration and evocation of the memories of all those who have made the smuggling activity of survival of the community.

Inserted in the donjon of the Castle, this museum houses some architectural elements and crafts collected in the village and the surrounding area, attributable to a period of transition between the 6th and 9TH in the arms room covered with a rib vault of warheads. In the upper room, an exhibition programme dedicated to the history of the fortress itself.

Miner's House – documentation centre is the first permanent pole of the São Domingos mine Museum. Its construction was the initial contribution to the reconstruction and recovery of the mining village. Associate in this space two features: the museums, with the re-creation of the miner's House and the memory collection, with the installation of the documentation centre. Miner's House shows the physical reality of the living space of a mining family. The objects, the memories, the symbols and the shortcomings are there represented. Above all, plan to lead the visitor's imagination and sensitivity so that it can find the daily …