Teleost fish play important roles in aquatic ecosystems and aquaculture. Here, we sequenced and assembled the genome of the first threadfin fish, the fourfinger threadfin Eleutheronema tetradactylum (Perciformes: Polynemidae). Threadfins show a range of interesting biology, and are of considerable importance in both wild fisheries and aquaculture. Additionally, E. tetradactylum is of conservation relevance since its populations are considered to be in rapid decline and it is currently classified as endangered. We provide a genome assembly for E. tetradactylum with high contiguity (scaffold N50 = 56.3 kb) and high BUSCO completeness at 96.5%. The assembled genome size of E. tetradactylum is just 610.5 Mb, making it the second smallest perciform genome assembled to date, and only ~9.68% of the sequence was found to consist of repetitive elements, making this the lowest repeat content identified to date for any perciform fish. A total of 37,683 protein-coding genes were annotated, including analyses of developmental transcription factors, including Hox, ParaHox, and Sox families. MicroRNA genes were also annotated and compared with other chordate lineages, elucidating the gains and losses of chordate microRNAs. Our findings provide a useful genomic resource for future research into the interesting biology and evolution of this important group food fish.