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In this study, specimens of the large-scale sand smelts Atherina boyeri, a fish species occurring in different environments (freshwater lakes, coastal lagoons, sea), were examined for their body shape and the differences observed were analysed statistically. The variation of external morphology was investigated in 11 populations from different environments. The morphology was characterized by means of geometric morphometrics and compared; results showed that the phenotypic (morphometric) distances among samples differed significantly by Relative Warp Analysis, specimens from the coastal lagoon being clearly separated from those belonging to lake and marine populations on the first RW1 axis and the latter ones separated on the RW2 axis. The results obtained also show the absence of a gradient of shape differences according to lake–lagoon–sea origin or eidonomic convergence in fish from environments with similar (high) trophic productivity. An integration of geometric morphometric data in a multidisciplinary approach with genetic, biochemical, geographical, molecular and other morphological analyses is necessary to describe the phylogenetic relationships of Atherinidae, shedding light on some ambiguous taxonomic ranks. [ABSTRACT FROM PUBLISHER]