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The predicted sequence for thousands of genes revealed by a preliminary low-coverage genome assembly is presented for Brycon orbignyanus, an endangered migratory fish. Neotropical migratory fish stocks have been drastically reduced due to accumulated environmental pressure. Brycon orbignyanus, once one of the main fisheries species in the Platine Basin, is now very rare in nature and relies on spawning programs and a few well preserved or still untouched sites. The use of high-throughput DNA sequencing is still untapped regarding the functional genome information from B. orbignyanus. In order to help bridging this gap, we present a dataset resulting from the first functional annotation from a de novo genome assembly for B. orbignyanus, from short reads (90 bp), obtained by the HiSeq 2000 platform (Illumina). The annotation was performed for scaffolds over 10 kb using the Maker pipeline, with reference sequences taken from the NCBI for the Characiformes order. This annotation resulted in the prediction of 12,734 genes, classified with the aid of PANTHER. The data presented here can facilitate the development of basic research in this threatened species, along with practical biotechnological tools for different areas, such as commercial and environmental fish spawning operations (e.g. hormonal induction, growth) and human health.