This research represents the first approach to the study of the shelf zooplankton community at a Mediterranean scale, using acoustic standardized data collected in June-July in 10 different geographical sub-areas (GSAs) established by the General Fisheries Commission for the Mediterranean (GFCM) within the framework of the MEDiterranean International Acoustic Survey (MEDIAS). The analysis of the zooplankton layers based on their acoustic characteristics has revealed the potential of these surveys for the study of zooplankton at a Mediterranean basin scale and, also, the need to collect biological samples to interpret the acoustic records in terms of species. The fish population’s direct assessment is established in the MEDIAS framework, but the integration of zooplankton community data would constitute a qualitative step for the understanding of the fluctuations of fish populations and therefore to achieve the objective of an ecosystem-based management. Results have revealed the ubiquity of the zooplankton layers and its ability to form layers detectable by scientific echosounders throughout the Mediterranean at the common fish assessment frequency (38 kHz). In addition, the use of two frequencies (38 and 120 kHz) has allowed to apply the dB difference method, observing changes in the difference of the Mean Volume Backscattering Strength (∆MVBS) at 38 and 120 kHz frequencies, which would be related to changes in the composition of the zooplankton community.