Gelatinous zooplankton species composition, distribution and abundance were investigated in the bay and the lagoon of Bizerte (North Tunisian coast) from January 2004 to December 2005. In total, 48 species were identified in the study area: 24 medusae, 11 siphonophores, four appendicularians, six chaetognaths, two pteropods and one doliolid. The hydromedusa Eutima mira was recorded for the first time in the Western Mediterranean Sea. The diversity in the Bay of Bizerte was greater than the diversity in the Bizerte lagoon. There was a loss of species diversity. Siphonophores were the most sensitive group to anthropogenic discharge. Only two species of siphonophores were recorded in the lagoon. Four species of gelatinous zooplankton, Muggiaea kochi, Lensia conoidea, Oikopleura longicauda and Podocorynoides minima were the most frequent species in the lagoon and may benefit from eutrophication. Appendicularians were numerically the most dominant group in the bay and the lagoon of Bizerte. Mesozooplankton density declined significantly in autumn and winter of 2004 and 2005 in relation to the dense aggregations of the scyphomedusae Pelagia noctiluca. Statistical analysis divided the study area into three zones: lagoon zone, bay zone and channel zone.