The Texas Parks and Wildlife Department raises Southern Flounder (Paralichthys lethostigma) for stock enhancement on the Texas coast . Information on molecular markers is currently lacking and is needed to help improve the culture of Southern Flounder. Potential application s include screening of broodstock and selection for beneficial characteristics (i.e. increased tolerance of variable estuarine environments, normal pigmentation ), identification of hormones or physical treatments to induce metamorphosis , and the appropriate temperature to produce female-biased fingerlings . Pre-metamorphic Southern Flounder larvae were used to generate 289,367,813 raw nucleotide reads using next generation RNA sequencing on an Illumina HighSeq 2000 platform of 21 libraries, prepared with RNA from Southern Flounder . A total of 329,198 short read sequences were produced and 96.48% were mapped to assemble a "De novo S outhern Flounder pre-metamorphic larvae transcriptome". The quantitative measures indicated that 81.3% of the transcriptome assemblages were complete, 7.7 % were fragmented, and 11.0 % were missing. Gene identification, function, annotation, and differential gene expression were measured and showed statistical significance (at P value 0.001) of expressed genes. Identified genes include sex determination, metamorphosis, pigmentation, salinity, and temperature tolerances; as well as antifreeze proteins and metabolic genes related to growth and stress responses. Preliminary results of the induction of metamorphosis on larvae using Thyroxines will be presented.