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Rays and skates are an unavoidable part of the by-catch in demersal fisheries. Over the past 40 years, the thornback ray (Raja clavata) has decreased in numbers and even disappeared in some areas, leading to concerns about genetic risk. For this reason, the effective population size (Ne), the migration rate (m) and temporal changes in the genetic diversity were estimated for the population of thornback rays in the Irish Sea and Bristol Channel. Using genotyped, archived and contemporary samples (1965 and 2003–2004), Ne was estimated at 283 individuals (95% CI=145–857), m at 0.1 (95% CI=0.03–0.25) and the Ne/N ratio between 9 × 10–5 and 6 × 10−4. Although these results must be treated with caution, due to the small sample sizes, this is the first attempt to estimate Ne in an elasmobranch species. The low Ne/N ratio suggests that relatively few individuals contribute to the next generation. The combined effect of sex bias, inbreeding, fluctuations in population size and, perhaps most important, the variance in reproductive success may explain the low Ne/N ratio. In addition, the relatively high gene flow between Irish Sea population and other source populations is likely to have had an impact on our estimate, which may be more relevant at the metapopulation scale. No significant loss of genetic diversity was found over the 40-year timeframe and long-term maintenance of the genetic diversity could be due to gene flow.Heredity (2008) 101, 120–126; doi:10.1038/hdy.2008.36; published online 7 May 2008 [ABSTRACT FROM AUTHOR]