The NaGISA project (Natural Geography Ιn Shore Areas) is a global initiative within the framework of the Census of Marine Life. The Mediterranean Sea has joined with 4 stations, 2 in Italy and 2 on the island of Crete, Greece. Two different sites were sampled during two consecutive years (2007 and 2008) by means of SCUBA diving. On the basis of the evidence offered by the collected material from the hard substrates of Crete, and the literature mined datasets concerning the molluscan assemblages, two main issues are investigated: (a) is the molluscan fauna sampled in the two NaGISA sites representative of the regional Mediterranean one? and (b), is the molluscan fauna sampled from the two sites randomly assembled from the regional species pool across different spatial scales? Although a strong tendency of the local molluskan composition to be randomly sampled from the regional pools at all scales, it is not possible to demonstrate with a degree of certainty whether their observed local diversity is independent of local and regional processes or if it is determined by a combination of the two acting either in concert or antagonistically.