Teleost fish underwent whole genome duplication around 450 million years ago followed by diploidisation and loss of 80-85% of the duplicated genes. To identify a deep signature of this teleost-specific whole genome duplication (TSGD) we searched for duplicated genes that were systematically and uniquely retained in one or other of the super-orders Ostariophysi and Acanthopterygii. TSGD paralogues comprised 17-21% of total gene content. Some 2.6% (510) of TSGD paralogues were present as pairs in the Ostariophysi genomes of Danio rerio (Cypriniformes) and Astyanax mexicanus (Characiformes), but not in species from 4 orders of Acanthopterygii (Gasterosteiformes, Gasterosteus aculeatus; Tetraodontiformes, Tetraodon nigroviridis; Perciformes, Oreochromis niloticus and Beloniformes, Oryzias latipes) where a single copy was identified. Similarly, 1.3% (418) of total gene number represented cases where TSGD paralogues pairs were systematically retained in the Acanthopterygian, but conserved as a single copy in Ostariophysi genomes. We confirmed the generality of these results by phylogenetic and synteny analysis of 40 randomly selected linage specific TSGD paralogues (LSPs) completed with the transcriptomes of three additional Ostariophysi species (Ictalurus punctatus (Siluriformes), Synocyclocheilus species (Cypriniformes) and Piaractus mesopotamicus (Characiformes)). No chromosome bias was detected in TSGD paralogue retention. Gene ontology (GO) analysis revealed significant enrichment of GO terms relative to the human GO SLIM database for "growth", "Cell differentiation" and "Embryo development" in Ostariophysi and for "Transport", "Signal Transduction" and "Vesicle mediated transport" in Acanthopterygii. The observed patterns of paralogue retention are consistent with different diploidisation outcomes having contributed to the evolution/diversification of each super-order.