The concept of ‘effective population size’ (N e ), which quantifies how quickly a population will lose genetic variability, is one of the most important contributions of theoretical evolutionary biology to practical conservation management. N e is often much lower than actual population size: how much so depends on key life history and demographic parameters, such as mating systems and population connectivity, that often remain unknown for species of conservation concern. Molecular techniques allow the indirect study of these parameters, as well as the estimation of current and historical N e . Here, we use genotyping to assess the genetic health of an important population of the critically endangered hawksbill turtle (Eretmochelys imbricata), a slow-to-mature, difficult-to-observe species with a long history of severe overhunting. Our results were surprisingly positive: we found that the study population, located in the Republic of Seychelles, Indian Ocean, has a relatively large N e , estimated to exceed 1000, and showed no evidence of a recent reduction in N e (i.e. no genetic bottleneck). Furthermore, molecular inferences suggest the species' mating system is conducive to maintaining a large N e , with a relatively large and widely distributed male population promoting considerable gene flow amongst nesting sites across the Seychelles area. This may also be reinforced by the movement of females between nesting sites. Our study underlines how molecular techniques can help to inform conservation biology. In this case our results suggest that this important hawksbill population is starting from a relatively strong position as it faces new challenges, such as global climate change.