In many vertebrates, sex of offspring is determined by external environmental cues rather than by sex chromosomes. In reptiles, for instance, temperature-dependent sex determination (TSD) is common. Despite decades of work, the mechanism by which temperature is converted into a sex-determining signal remains mysterious. This is partly because it is difficult to distinguish the primary molecular events of TSD from the confounding downstream signatures of sexual differentiation. Here we use the Australian central bearded dragon, in which chromosomal sex determination is overridden at high temperatures to produce sex-reversed female offspring, as a unique model to identify TSD-specific features of the transcriptome. The link between epigenetic regulation and external temperature appears to involve an unusual mode of gene regulation (differential intron retention) in a family of chromatin-modifying genes that are key players in eukaryotic epigenetic regulation. Significantly, we also observe sex-associated differential retention of the equivalent introns in the same chromatin-modifying gene transcripts expressed in embryonic gonads from other reptiles, indicative of a reptile-wide mechanism controlling TSD. This work is soon to appear in Science Advances.