In vertebrates, a remarkable diversity of sex determining mechanisms is observed, ranging from environmental to genetic sex determination (ESD and GSD). In teleosts, sex determination mechanisms include both environmental and genetic regulation and are extremely diverse, changeable, and labile. In addition, many sex-determining genes have been already found in this group of vertebrates showing that SD genes can be extremely variable even between closely related organisms. Hence, teleost fish have emerged as interesting models to study the macroevolution of sex determining (SD) mechanisms within vertebrates. The cavefish Astyanax mexicanus belongs to the Characiform group. Different populations of Astyanax have been described, including pigmented river-dwelling and several depigmented blind cave populations. These populations are still inter-fertile and cave populations are known to have evolved from a surface ancestral population around 100,000 years ago. In addition these Astyanax populations can be also reared under laboratory conditions quite easily and are amendable to genetic manipulations. Altogether this makes surface and cave populations a particularly interesting evolutionary genetic model system for comparative and microevolution studies. We thus initiated studies on the microevolution of SD and SD genes in the cavefish Astyanax mexicanus, and used restriction site-associated DNA (RAD) sequencing and pool-sequencing approaches to identify sex-biased molecular markers in both cave and surface populations. Our first results led to the identification of a candidate master sex-determining gene that potentially triggers SD in both cave and surface populations. Despite this conservation of a strict GSD and the same master sex-determining gene, our results also pin point that SD in Astyanax mexicanus has already evolved between surface and cave populations and suggest a quick evolutionary transition between an old polygenic SD system in surface population towards a more recent and simple monofactorial system in cave population.