Coralligenous bioconstructions are one of the Mediterranean’s most distinctive and biodiverse marine habitats. This research aimed to provide a preliminary characterization of macrobenthic coralligenous assemblages at four sites located in the Marine National Park of Karaburun-Sazan in Albania. We analyzed images obtained from videos recorded along underwater transects at two different depths. Over a total of 61 taxa (3 Rhodophyta, 2 Ochrophyta, 6 Chlorophyta, 30 Porifera, 5 Cnidaria, 3 Mollusca, 2 Annelida, 1 Arthropoda, 4 Bryozoa, 4 Echinodermata, and 1 Chordata), 53 were identified at the species level using taxonomic and semi-quantitative video image analysis, thus allowing an update to the Albanian coralligenous species list with 34 new species. This study revealed differences in species richness and composition among the investigated sites and between depths, with a high number of taxa exclusive to one site and a few taxa common to all sites. Seven taxa are protected by law, among which are the echinoderm Centrostephanus longispinus, included in the Bern (Annex II) and Barcelona (Annex II) Conventions and Habitat Directive (92/43 EEC) (Annex IV), and the sponges Spongia (Spongia) officinalis and S. (S.) lamella, included in Annex III of the Bern Convention. Only the alga Caulerpa cylindracea can be considered an alien species. Although preliminary, the present research indicated the occurrence of rich and diversified macrobenthic assemblages in the study area. Moreover, it has been demonstrated that video analysis can provide a biodiversity baseline within MPAs, where traditional methods involving invasive sampling cannot be applied, particularly in areas such as the Albanian coasts, where anthropogenic impacts have been historically significant. Finally, this work provides a first estimate of the structural biodiversity in a recently established marine protected area, thus representing the basis for subsequent monitoring.