From 1895 to 1934 Paolo Orsi directed the museum, but the increasing number of finds made a new space necessary at the current location in the garden of the villa Landolina. The new museum space, designed by the architect Franco Minissi was inaugurated in January 1988, with two floors of 9,0002. Initially only one floor and a basement of 3,000 m2 containing an auditorium were open to the public.
In 2006, a new exhibition area on the upper floor was inaugurated, dedicated to the classical period, but more space still remained unused. In 2014 a final expansion allowed the display of the Sarcophagus of Adelphia and other finds from the catacombs of Syracuse.
The museum contains artefacts from the prehistoric, Greek and Roman periods found in archaeological excavations in the city and other sites in Sicily.
Sector A is dedicated to the prehistoric (Upper Palaeolithic-Iron Age) with a display of rocks and fossils which testify to the various animals found in Sicily in the Quaternary. It is preceded by a section which displays the geological characteristics of the Mediterranean Sea and the Iblean zone.
In sector B, dedicated to the Greek colonies in Sicily from the Ionic and Doric period, it is possible to see the locations of the Greek colonies in Sicily and their respective mother cities. Also on display: a headless marble statue of a Kouros, found at Leontini from the fifth century BC. a bone kourotrophos, a headless female statue, holding two twins, which was found at Megara Hyblaea. votive statues of Demeter and Kore and a gorgon from the Doric colony at Megara Hyblaea a head of Augustus found at Centuripe.
In sector C there are finds from the colonies of Syracuse: Akrai (664 BC), Kasmenai (644 BC), Camarina (598 BC), Eloro, as well as finds from other centres of eastern Sicily, Gela ed Agrigento.
Sector D, located on the upper floor and inaugurated in 2006, contains finds from the Hellenistic and Roman periods. It contains two of the most celebrated pieces in the museum, the Sarcophagus of Adelphia and the Venus Anadiomene, also called Venus Landolina after the location of its discovery, found in Syracuse in 1804 and described by Bernabò Brea as “for the excellence of its sculpting, an exquisite treatment of the naked form, of incredibly liveliness and softness”. Moreover, a selection of coins from the numismatic cabinet of the piazza Duomo is on display.