In this paper we present the ZooCAM, a system designed to digitize and analyse on board large volume samples of preserved and living metazooplankton (i.e. multicellular zooplankton) and fish eggs > 300 µm ESD. The ZooCAM has been specifically designed to overcome the difficulties to analyse zooplankton and fish eggs in the framework of the PELGAS survey, and provide high frequency data. The ZooCAM fish eggs counts were comparable to those done with a dissecting microscope. The ZooCAM enabled the accurate prediction and fast on board validation of staged anchovy and sardine eggs in almost real time after collection. A comparison with the ZooScan, on a more complex zooplanktonic community, provided encouraging results on the agreement between the 2 instruments. ZooCAM and ZooScan enabled the identification of similar communities and produced similar total zooplankton abundances, size distributions, and size spectra slopes, when tested on the same samples. However these results need to be further refined due to the small number of samples used to compare the two instruments. The main ZooCAM drawback resides in a slight but sensible underestimation of abundances and sizes, and therefore individual and community biovolumes. The ZooCAM have been successfully deployed over 4 years, on numerous surveys without suffering any major failure. When used in line with the CUFES it provided high resolution maps of staged fish eggs and zooplanktonic functional groups. Hence the ZooCAM is an appropriate tool for the development of on board, high frequency, high spatial coverage zooplanktonic and ecosystemic studies. Highlights ► The ZooCAM is a new inflow imaging system for fast onboard counting, sizing and classification of fish eggs and metazooplankton. ► The ZooCAM has been used on-board for 4 years without suffering any failure and enabled the analysis ∼10,000 samples so far (CUFES, WP2 and other plankton nets). ► The ZooCAM provided staged fish eggs counts that were equivalent to those traditionally done by microscopic examination. These data were used for 2016 and 2017 anchovy and sardine stocks estimations in the Bay of Biscay (DEPM method) ► The ZooCAM enable the real time, on-board, imaging of complex communities zooplankton samples and provide results comparable to on-land, well established counterpart, the ZooScan. ► The ZooCAM is a valuable tool to improve zooplanktonic studies, in term of spatial coverage and temporal frequency, to perform ecosystemic studies.