Sex of Nile tilapia is determined genetically by sex chromosomes following an XX/XY system, but temperature can override it. High temperatures >32°C applied during early sex-differentiation can induce a female to male sex reversal producing functional testis and a male reproductive behaviour. Nile tilapia aquaculture relies on all-males farming due to male's better growth-rate and as a means to control reproduction. Currently, the large majority of the all-male productions are obtained through androgen treatments. Temperature-induced masculinisation is a feasible and a much more sustainable method to produce all-male offspring. The male proportion induced by temperature (the thermosensitivity) is an inherited trait. To characterise this thermosensitivity, we searched for the genetic basis using double digest Restriction Associated DNA (ddRAD) sequencing on controlled-reared families sired from wild-caught individuals from Lake Kou (Burkina Faso). We found association of several linkage groups. In addition, we studied possible mechanisms involved in the temperature-induced masculinisation in the testis, analysing epigenetic and transcriptome responses. For this, two genetically different families were treated to 36°C and 27°C during their sex-differentiating stage. At 90 days post-fertilization, Family K14 had a 90% male proportion whereas, Family K13 only showed 59.8% males. Differences in DNA methylation levels persisted in adult ovaries and testis. Our MeDIP-Seq analyses predicted 26,339 CpG islands with presumably low methylation, and identified 77,427 regions of high methylation in K14 and 63,168 regions in K13. Our findings indicate that in contrast to CGI methylation, the bulk methylome of the phenotypically plastic K14 family reacts strongly to temperature increase while the K13 family with low phenotypic plasticity remains stable. We found 964 differentially methylated regions (DMR) between XY males and XX females in the thermosensitive K14 family whereas K1