Here we presented changes in the non-crustacean zooplankton community in the years characterized by the large scale changes in the thermohaline circulation in the East Mediterranean known as the Eastern Mediterranean transient (EMT) and stronger inflow of colder and less saline Modified Atlantic Water (MAW) into the Adriatic Sea. Monthly samplings from February 1995 to February 1996, were performed at fixed station Stoncica near the Island of Vis in the open oligotrophic Middle Adriatic waters. Zooplankton samples, taken vertically from 100 m to the surface using a Nansen net with 125- mu m mesh size were analyzed in detail for the following zooplankton taxa: Hydromedusae, Calycophorae, Ctenophora, Pteropoda, Heteropoda, Polychaeta and Chaetognatha. Among the investigated non-crustacean zooplankton three species were registered for the first time, while one species reappeared after years of absence. Compared with earlier data there was a dramatic change in dominant species of calycophoran medusae, pteropods and polychaetes. Data presented herein provide baseline information that is essential for the evaluation of impact of hydroclimatic changes on the zooplankton community, which started in the East Mediterranean in the 1990s and are still on going.