The Centre for Cultural Informatics of the Information Systems Laboratory (ISL-CCI) in the framework of the project "Innovative ICT applications and use of emerging technologies at the Archaeological Museum of Messara, aiming at extroversion and the promotion of the Digital Cultural Resources of the Region of Crete", undertook the design and implementation of the Web Portal and the Digital Repository of the Archaeological Museum of Messara. For this purpose, the "Scientific Documentation and Website Content Management System" was developed, based on the "Synthesis-Core" software developed by the Cultural Informatics Centre (CCI) and the web portal system of the Archaeological Museum of Messara, which is available to public at https://www.messaramuseum.gr. In addition, the interface of this system with the thesaurus system - THEMAS of the CCI for the management of the thesaurus of terms for the types of monuments developed by Ephorate of Antiquities of Heraklion (EFAI) was implemented. Also in the framework of the project, the scientific data of the repository were automatically converted into Linked Open Data and stored in the state-of-the-art semantic network system (rdf/rdfs) AQUB of the Centre for Cultural Informatics. This system offers the interested researcher the possibility to navigate and submit scientific queries on this data based on the international cultural ontology CIDOC-CRM (ISO Standard 21127:2014, https://www.cidoc-crm.org/). The Scientific Documentation and Content Management System, the THEMAS thesaurus system and the AQUB semantic network system are accessible with controlled access through the central management environment of the Archaeological Museum of Messara developed in the framework of this project. The implementation of the digital repository and the web portal of the Archaeological Museum of Messara was funded by the Operational Programme "Crete" of the NSRF 2014-2020.