For many reptiles, sex is determined by the incubation temperature of the egg during embryonic development, a process known as temperature-dependent sex determination (TSD). Previous studies in reptiles with TSD have examined homologs of genes that play a role in sex determination in mammals. However, the traditional candidate gene method lacks the ability to discover novel sex-determining genes and sometimes can be misleading. To complement the candidate gene method and accelerate progress in the field of TSD, we conducted a transcriptome-wide analysis of gene expression and gene function using next generation sequencing technology. We constructed and annotated a reference transcriptome for the common snapping turtle, Chelydra serpentina, one of the most widespread and abundant turtles in North America. With differential gene expression analysis comparing gonadal transciptomes between male-producing and female-producing temperatures, we identified several hundred candidate genes for TSD. With these genes, we reconstructed a gene regulatory network underlying TSD using the algorithm for the reconstruction of accurate cellular networks (ARACNe), an algorithm that is able to identify direct gene-gene interaction with high precision and sensitivity. Our transcriptome analyses not only shed new light on the study of TSD but also offer important insights into sexual development in all vertebrates and sex associated disorders in humans.