Recent research in island biogeography has highlighted the important role of late Quaternary sea‐level fluctuations in shaping biogeographic patterns in insular systems but focused on oceanic systems. Through this study, we aim investigate how late Quaternary sea‐level fluctuations shaped species richness patterns in continental‐shelf island systems. Focusing on the Aegean archipelago, we first compiled maps of the area’s geography using published data, under three sea‐level stands: (a) current; (b) median sea‐level over the last nine glacial–interglacial cycles (MSL); and (c) Last Glacial Maximum (LGM). We gathered taxon–island occurrences for multiple chorotypes of angiosperms, butterflies, centipedes, and reptiles. We investigated the impact of present‐day and past geographic settings on chorological groups by analyzing island species–area relationships (ISARs) and using generalized linear mixed …