In reptiles with temperature-dependent sex determination, gonadogenesis is initially directed by the incubation temperature of the egg during the middle third of embryonic development. The mechanism by which temperature is transduced into a sex-determining molecular signal remains a mystery, and here we examine the molecular network underlying sex determination in gonads in vitro. We use a whole organ culture system to show that expression of putative members of the sex-determining network (Dmrt1, Sox9, Mis, and FoxL2) are regulated by temperature endogenously within cells in the bipotential gonad and do not require other embryonic tissues to be expressed in a normal pattern in the red-eared slider turtle, Trachemys scripta. Furthermore, following a change in temperature, these factors exhibit temperature-responsive expression patterns that last for the duration of gonadogenesis. Finally, mosaic misexpression of a fusion Sox9 construct demonstrates the ability to functionally manipulate the gonad at the molecular level.