The Neosho madtom (Noturus placidus) is a small catfish, generally less than 3 inches in length, unique to the Neosho-Spring River system within the Arkansas River Basin. It was federally listed as threatened in 1990, largely due to habitat loss. As part of conservation efforts, we generated whole genome Illumina paired-end sequence data from ten Neosho madtom (average 39X coverage) originating from three geographically separated subpopulations to evaluate genetic diversity and population structure. One slender madtom (Noturus exilis) was also sequenced as an outgroup. Lack of a reference genome necessitated variants be discovered using De Bruijn graphs implemented in CORTEX v1.0.5.21. Approximately 1.64 million high confidence single nucleotide polymorphisms (SNPs) were observed. Only 86,155 SNPs were variable across the Neosho madtoms sequenced, indicating overall low level genetic diversity. While principal component analysis based on these genotypes accurately clustered individuals from the same location together, insignificant eigenvalues indicated weak population structure, suggesting these subpopulations are genetically compatible for reintroduction among these three locations. We also completed a draft de novo assembly of the Neosho madtom genome from 120X of sequences pooled across 3 individuals. We assembled the ~1 Gb genome into 149,885 contigs with a N50 of 12,261 bp. Using only 50X coverage of paired-end and mate pair data from a single fish, we were able to assemble the genome into 68,147 scaffolds with an scaffold N50 of 120 kb, demonstrating the value in assembling a genome from a population that is closely related to a species of economic interest (i.e., channel catfish, Ictalurus punctatus) but has lower genetic diversity and is easier to assemble. Ongoing efforts aim to improve the assembly by using sequences from DISCOVAR recipe libraries (250 bp paired-end reads), assembled with DISCOVAR de novo and MaSuRCA. The ability to generate a reference genome allows us to use demographic models, such as PSMC, to compare the effective population sizes between the Neosho madtom and the slender madtom. With genomic tools developed, we can now better manage this endangered species and investigate the basic biology of why such a low-diversity species can subsist.