Tilapia is the second most produced fish in aquaculture world-wide. In Nile tilapia (Oreochromis niloticus) the phenotypic sex can be determined through (interaction of) minor autosomal factors, a major male determining factor, and environmental factors. Even though intensive aquaculture farming often results in rapid breeding and stunted populations, synthetic hormones allow the production of mono-sex male broods. However, showcasing tilapia as the first aquaculture fish species certified by the Aquaculture Stewardship Council, this emphasizes the need for more sustainable sex control protocols. As such, a temperature treatment of the fry might be a future alternative. A prerequisite for adoption of this technique would be the reliable identification of temperature-responsive individuals. This could be achieved through the use of pertinent genetic markers. Therefore, the aim of the present work was to investigate global gene expression using RNA-seq as well as candidate genes during temperature-dependent sex reversal. Genetic female and genetic male families were established. After yolk sac absorption, larvae were randomly distributed into two groups. Temperature in the control groups was kept at 28 degrees C, whereas treatment groups were reared at 36 degrees C from 10 to 20 days post fertilization. For the investigation of the transcriptome, tissue samples were collected at 10, 14, 17, and 19 days post fertilisation. Sex and morphometric parameters were assessed on the remaining full-sibs. Zfand3, a putative testis determining factor, was among the most strongly differentially expressed genes at day 17 post fertilization. Further, among candidate genes (cyp19a1, amh, amhrII and fst) only subtle differences between genetically female control and treatment groups were detected. Only cyp19a1a showed a slightly lower expression in control groups when compared to the treatment groups (-0,32). In genetically male groups cyp19a1a was strongly up-regulated at day 14, 17, and 19 when compared to the control (+4,8; +81,1; +15,1).