A growing number of studies report an increase in jellyfish populations worldwide that may have consequences for marine planktonic food web dynamics. The principal objective of this study was to understand the changes in a zooplankton community during blooms of Liriope tetraphylla and subsequent mucilage events in the Sea of Marmara, a small highly stratified transitional basin between the Black and Aegean Seas. Liriope blooms observed in 2006 and 2007 reached a maximum abundance of 2978 ind.·m−3, following the species' first observation in 2005. Jellyfish species are known to play a key guild role by restructuring plankton communities and in the Sea of Marmara Liriope caused a temporal regime shift from a crustacean- to a jellyfish-controlled system. A rapid decline in abundance of most important zooplankton species followed the Liriope increase, together with a drastic shift in community structure. The dominant summer–autumn species Penilia avirostris (Cladocera) vanished in the autumn of 2006 and was diminished ~30-fold in 2007 when compared with years without Liriope. The decline in zooplankton and the devastating effects of mucilage on pelagic ecosystem and socio-economics through restricting commercial fisheries implied sensitivity of the already perturbed Marmara ecosystem to changes in predator densities and environmental stability.