Fishery production is highly dependent on fish growth and environmental factors; primary production and temperature are the two most important variables affecting almost all biological rates, especially individual growth or population production rate. The growth of European anchovy, Engraulis encrasicolus, was compared between two populations inhabiting different ecosystems: the Tyrrhenian Sea, characterized by riverine inputs and the Strait of Sicily, an oligotrophic area. The effects of habitat conditions on growth was also evaluated using literature data on other of European anchovy populations. Water temperature was confirmed to be a determinant factor for anchovy growth at the species level positively affecting the length at age-1. On the contrary, a negative relationship was found between chlorophyll-a and the length at age-1. These findings suggested that size at age-1 is strongly dependent on habitat conditions. The age structure differed significantly between the two populations, with the Tyrrhenian stock dominated by age-1 fish.