This paper concerns the changes occurred over both decennial and millennial spans of time in a sponge assemblage present in coralligenous biogenic build-ups growing at 15 m depth in the Ligurian Sea (Western Mediterranean). The comparison of the sponge diversity after a time interval of about 40 years (1973-2014) showed a significant reduction in species richness (about 45%). This decrease affected mainly the massive/erect sponges, and in particular the subclass Keratosa, with a species loss of 67%, while the encrusting and cavity dwelling sponges lost the 36% and 50%, respectively. The boring sponges lost only one species (25%). This changing pattern suggested that the inner habitat of the bioconstructions was less affected by the variations of the environmental conditions or by the human pressures which, on the contrary, strongly affected the species living on the surface of the biogenic build-ups. Five cores extracted from the bioherms, dating back to 3500 YBP, allowed to analyse the siliceous spicules remained trapped in them in order to obtain taxonomic information. Changes at generic level in diversity and abundance were observed at 500/250-years intervals, ranging between 19 and 33 genera. The number of genera showed a sharp decrease since 3500-3000 to 3000-2500 YBP. After this period, the genera regularly increased until 1500-1250 YBP, from when they progressively decreased until 1000-500 YBP. Tentatively, these changes could be related to the different climatic periods that followed one another in the Mediterranean area within the considered time span. The recent depletion in sponge richness recorded in the Ligurian coralligenous can be considered relevant. In fact, the analysis of the spicules indicated that the sponges living in these coralligenous habitats remained enough stable during 3000 years, but could have lost a significant part of their biodiversity in the last decades, coinciding with a series of warming episodes.