Wild organisms live in complex environments of stratified habitats with specific chemophysical characteristics such as temperature, and develop preferences to adequate niches for setting optimal thermal body regulation. But what about biological settings when thermal environment is not a choice for living? An increasing number of species are rapidly confronted to inadequate thermal habitats consequently to climate change. Ectothermic animals such as fishes, which only rely on environmental temperatures, are particularly affected. However, little is known on how lasting thermal changes of niches affect the genetic architecture of key physiological functions and how temperature preference evolves. Thus, we propose an integrative and longitudinal approach in the lab and in the wild using a unique fish model for genetic studies: the Astyanax mexicanus. Changes in water levels isolated some individuals usually living in hot rivers of Central America (surface morph) into temperate caves. To face such a drastic environmental transformation a cave-adapted blind morph evolved, displaying striking adaptations in morphology, physiology and behavior. We question whether the temperature preference behavior evolved between the two morphs of this single species and what are the related genetic markers. We choose a quantitative trait loci approach to associate genetic variations with individual temperature preference behavior in animal freely swimming along a gradient ranging from 13°C to 37°C. In parallel, we aim at monitoring seasonal temperature variations and related chemophysical water parameters of 5 river and cave sites by deploying autonomous probes over a complete year to provide unprecedented look at the natural habitat of each Astyanax morph. Understanding thermal acclimation at a genetic level will provide insights on the altered biological settings and how mechanisms can reset these changes to a new operational level.