Background: Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They share similar phenotypic changes such as blindness and depigmentation that are the result of independent and convergent evolution. In particular they allow to examine whether their evolution involved the fixation of standing genetic variation and/or de novo mutations. Cavefish populations are currently assigned to two main groups, the so-called "old" and "new" lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations. Results: First, we reanalyzed published mitochondrial DNA and microsatellite polymorphism and we found that these data do not unambiguously support an ancient origin of the old lineage. Second, we identified a large number of single-nucleotide polymorphisms (SNPs) in transcript sequences of two pools of embryos (Pool-seq) belonging to the "old" Pachón cave population and a surface population of Texas. Based on the summary statistics that could be computed with these data, we developed a method in order to 1) detect a recently isolated small population and 2) estimate its age. This approach is based on the detection of a transient increase of the neutral substitution rate in such a population. Indeed Pachón cave population showed more neutral substitutions than the surface population, which could be a signature of its recent origin. Third, when we applied this method to estimate the age of the Pachón cave population which is considered one of the oldest and most isolated cavefish populations we found that it has been isolated less than 30,000 years, that is during the Late Pleistocene. Conclusions: Although it is often assumed that Pachón cavefish population has a very ancient origin, within the range of the late Miocene to the middle Pleistocene, a recent origin of this population is well supported by our analyses of DNA polymorphism as well as by other sources of evidence. It suggests that the many phenotypic changes observed in these cavefish would have mainly involved the fixation of genetic variants present in surface fish populations and within a short period of time.