Abstract The biodiversity of copepods as examined in the present study is based on an oceanographic survey conducted on two ecosystems along the Algerian coast (central and eastern) in the early autumn of 2014. During that investigation, the thermocline was present at shallow depth, extending between 30 and 80 m. A total of 49 species were recorded in the samples, belonging to 20 families, among which six families, Calanidae, Eucalanidae, Metridinidae, Oithonidae, Paracalanidae, and Temoridae, appeared to be dominant. The total abundance of zooplankton at the 13 stations was less than 600 ind/m3. Two geographic groupings have been distinguished: stations in the central sector (group 1) are in opposition to the other stations in the eastern sector (group 2). The quantitative levels of copepods are less abundant in the east (234.15 ind/m3) than in the centre (334.99 ind/m3). In the central regions, the trophic organization is dominated by omnivores (73.02%), with an inferior co-dominance of carnivores (14.02%) and herbivores (12.95%). In the east, copepods with omnivorous behaviour are strongly represented (82.14%), followed by phytophagous (13.85%) and carnivorous (4.01%) species. The distribution of the abundances over the copepod communities was found to be linked to the temperature, salinity, North Atlantic Oscillation (NAO) index, and phytoplankton biomass.