In this study we aim to examine and compare broad patterns of mitochondrial DNA variability and phylogeographic history in multiple species of marine fish from Portuguese waters and adjacent oceanographic regions. We will examine three different levels: 1) Regional-scale analyses of common species from NE Atlantic and Mediterranean Sea, 2) Global-scale analyses of cosmopolitan species shared between NE Atlantic and Australasia and 3) In-depth analyses of cryptic species, and phylogeography of Lepidopus caudatus and Zeus faber. We will use DNA barcodes of the mitochondrial gene cytochrome oxidase I for global and regional-scale analyses. Uncertainty in species differentiation will be tackled using complementary molecular markers (e.g. nuclear gene for rhodopsin), and collateral ecological information. Such a novel approach will greatly further our understanding of the spatial dynamics of marine fish and the evolutionary forces shaping their molecular variability. Retrieved information will improve the delineation of fish conservation and fisheries management strategies. As a result of the global and regional study above, we will build a DNA barcode library for identification of fish species occurring in Portuguese waters. This library will constitute a valuable resource with multiple applications for fisheries management, such as: 1) detection of cryptic species, 2) rigorous identification of eggs and larvae and consequent identification of spawning seasons and areas for multiple species, 3) improve detection of new occurrences and alterations in fish species ranges, 4) improving fish identification upon landing and consequently catch statistics, 5) identification of species in fish markets and 6) identification of fish species from fish parts or filets, among other applications.