In marine fish species, dispersal or migrations are known to be the principal forces responsible in minimizing population structure. Anadromous species show distinct genetical patterns linked to their specific reproductive behaviour. However, little is known about species that are marine spawners but use estuaries and freshwater as nurseries, such as Terapon jarbua, which is thought to be estuarine dependent and to form panmictic populations at a larger geographical scale. Nevertheless, patterns of hyposaline habitat use, larval homing behaviour, and site fidelity are considered to have the potential to separate populations or subpopulations. This study aims to understand the population structure of T. jarbua inhabiting coastal estuaries on Socotra island and the Yemen mainland, and to describe the associated fish communities and their ecology. Several hypotheses will be tested to demonstrate: 1) that T. jarbua is not an obligate user of estuaries but rather an “amphidromous” opportunistic species with regard to its use of coastal hyposaline habitats as nursery; 2) that T. jarbua forms a panmictic population between Socotra Island and South Yemen mainland, and, if this hypothesis is rejected; 3) that T. jarbua forms a panmictic population across the different estuarine habitats of Socotra Island. Inferred from otolith microchemistry, ”strains” that are geographically linked to distinct spawning and nursery habitats, are established to determine patterns and scales of connectivity between subpopulations living in hyposaline and marine habitats at different life stages (migrations, larval and mature stages, and spawning periods). The identity of the strains previously determined is tested by assessing the genetic differentiation between such strains using mitochondrial and microsatellite DNA variability and phenotypic characters.