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The Cyclades Islands (Aegean Sea, Greece) are part of the Mediterranean Basin biodiversity hotspot and harbor a plethora of endemic species. Plant communities on the smaller islands in this region have largely evolved in the absence of herbivory and frequently lack antiherbivore defenses. This study evaluates the short- and long-term effects of the European rabbit (Oryctolagus cuniculus), an herbivore that has been released on numerous islands in the region, by comparing islands that 1. have historically been rabbit-free (ungrazed); 2. are currently grazed by rabbits, and 3. have previously been grazed, but are now rabbit-free. Ecological impacts of rabbits on the Aegean Islands were investigated by assessing the abundance, composition, and diversity of plant and arthropod communities as well as soil characteristics. Our results indicate that ungrazed islands have more arthropod species, more specialized or endemic plant species, and less exposed soil than currently grazed islands. While ungrazed islands did not necessarily possess higher total plant species richness, they did harbor significantly more small-island endemic taxa relative to presently grazed islands. This study indicates that native plant communities on Mediterranean islets are not adapted to the presence of this introduced species and that the practice of intentionally releasing rabbits on islands has significant and lasting negative ecological impacts, especially on small islands. While a complete recovery of post-rabbit was not evident over the time span of our research, both arthropod and plant data indicate that partial recovery is possible once rabbits have been removed.