Atherina boyeri Risso, 1810 and A. presbyter Cuvier, 1829 show similar morphology and anatomy, which makes difficult the species identification by conventional tools. The ecological behaviour and biological features are markedly distinct in both species. In the Ria de Aveiro, a typical coastal estuarine lagoon, A. boyeri and A. presbyter are among the four most abundant species. Ecology, age and growth of both species were compared from sampling carried out from November 1998 to November 1999 at nine sites covering all the lagoon area. A. boyeri, a resident species, occurred in different stages of the lifespan in the entire lagoon area. Juveniles occurred dispersedly in space, with no apparent abiotic preference. In winter, older adults (2+-3+) occurred with high abundance at the edges of the lagoon, in deep regions with low temperature, salinity and transparency, and high dissolved oxygen and pH. During autumn, the juveniles of marine juvenile migrant species, A. presbyter, were confined to deep regions of the lagoon edges, with low temperature, salinity and transparency, high dissolved oxygen, and neutral pH. In mid-spring, the adults occurred with high abundance near the sea, in a narrow range of all abiotic parameters. The length frequency distribution, and the fish and otolith length-weight relationships were significantly different in both species. A. boyeri reached 11.6 cm in 3 years, while A. presbyter reached 15.1 cm in 4 years. For the same length, A. boyeri (b = 3.35) was heavier than A. presbyter (b = 3.09). The von Bertalanffy growth parameters for A. boyeri were L∞ = 11.6 cm, k = 0.099 year-1, and t0 = -3.797 years and for A. presbyter were L∞ = 15.8 cm, k = 0.138 year-1, and t0 = -2.501 years. A. boyeri and A. presbyter grew faster during the first year of life (66% and 43% of maximum size, respectively). The observed and theoretical length and age were quite similar for both species and the values close to those in different Atlantic and Mediterranean systems.