Genomics research is applied in selective breeding to improve the genetic quality of broodstock and seedstock for the U.S. warmwater marine finfish aquaculture industry. This pilot study originates from a long-term multidisciplinary project (USDA Agreement #59-6034-9-007) supporting the expansion of the U.S. warmwater marine finfish aquaculture industry. Florida pompano (Trachinotus carolinus) is our model species due to its consumer popularity, market value, and known capacity to spawn in captivity. We focus on developing techniques that will contribute to a DNA marker-assisted selection (MAS) breeding program and provide information on growth performance for T. carolinus in aquaculture. This study incorporates restriction-associated DNA (RAD) sequencing to analyze single nucleotide polymorphisms (SNPs) on genes linked to phenotypic traits such as growth and understand how these genetic markers relate to measurable morphological differences. The experiments were conducted in partnership with Aquaco Farms, in Fort Pierce, Florida. In response to the observation of atypical growth patterns among a particular cohort (progeny of known brood), we collected twenty fish 68 DPH (days post hatch) for comparative assessment and DNA extraction. Individual juveniles were collected and separated into two groups, ten with “normal” head sizes and ten with “abnormal” head sizes. Twelve types of morphological measurements were recorded for each fish “before” and “after” freezing the samples. DNA was extracted from fish fin clips for RAD sequencing on the Illumina HiSeq platform. Sequencing data will be analyzed for SNPs associated with growth differences using a variety of publicly available bioinformatics packages for RAD-Seq analysis.