Mediterranean coastal ecosystems experience many local and global stressors and require long-term monitoring to detect and follow trends in community structure. Between 2009 and 2017, we seasonally and annually monitored the spatiotemporal community dynamics at 11 sites on the rocky shores of the southeastern Mediterranean, focusing on the understudied intertidal vermetid reef ecosystem. Marked seasonal trends were found in biodiversity, with the highest diversity in winter and spring. Canopy-forming brown algae, dominating the northwestern Mediterranean intertidal reefs, were generally scarce on the reef platform and almost only found in tidepools. Interannual shifts in community structure were driven mostly by sharp fluctuations in a few dominant native and alien species and the regional mass mortality of an Indo-Pacific mussel in summer 2016. Compared to an older macroalgae dataset, dating back to 1973-1995, we found that some warm-affinity (summer) taxa became more dominant and cold-affinity (winter) species less dominant, while one once conspicuous species, Halimeda tuna, completely disappeared. The observed community shifts are probably driven mostly by stressors related to climate change. We encourage forming a network of long-term, multi-site ecological monitoring programs in the Mediterranean to improve our understanding of ecosystem change and to enable making better predictions at the basin scale.