This study includes a review of recently published results regarding zooplankton in the Boka Kotorska Bay (since 2009), and comparison of these results with earlier investigations. Non-loricate ciliates were the most numerous microzooplankton in spring 2013 (37%). Loricate ciliates (tintinnids) values were low and similar to those recorded in the open Adriatic Sea. However, their diversity was quite high: 20 estuarine–neritic and 26 species typical of the open sea were identified. Copepod nauplii were dominant metazoan microzooplankton component (32%). Seven phylums and 81 mesozooplankton taxa were determined. Copepods were the most dominant group. Among them, Oncaea–cyclopoids and Oithona nana were the dominant copepod taxa at all stations. Heterotrophic dinoflagellate Noctiluca scintillans and cladocera Penilia avirostris were often extremely numerous during warm seasons. Changes in the zooplankton community noted during recent investigations can be linked with the observed climate changes identified in the Adriatic and Mediterranean Sea since the 1990s, which are reflected in: (1) zooplankton high densities in the winter period with a lack of spring peak ; (2) domination of small-size cyclopoid copepods and decreasing of contribution of neritic calanoid species ; (3) prolongation of high Penilia avirostris abundance in the autumn period ; (4) spreading of invasive siphonophorae Muggiaea atlantica in the inner part of the Bay ; (5) frequent outbreaks of gelatinous zooplankton ; and (6) The first registered bloom of the ctenophore Bolinopsis vitrea in the Mediterranean in spring 2014, having a major impact on the regular planktonic food web system.