Fish have been highly exposed to radiation in freshwater systems after the Chernobyl Nuclear Power Plant (NPP) accident in 1986, and in freshwater and marine systems after the more recent Fukushima NPP accident in 2011. In the years after the accident the radioactivity levels rapidly declined due to the short half-life of some radionuclides and the decay of long-lived radionuclides. A recent study showed that, after several generations of exposure to environmental radiation at Chernobyl, perch displayed a delay in the maturation of gonads in the most contaminated lakes. Some undeveloped phenotypes were also observed in two of the three contaminated lakes. In order to gain insights into the long term effect of environmental low dose radiation on gonad development, a high throughput transcriptomic approach, including a de novo assembly, was applied to different gonad phenotypes of perch: normal from reference lake, apparently normal from low contaminated lake and apparently normal and undeveloped from more highly contaminated lakes.