Population viability might become compromised by the loss of genetic diversity and the accumulation of inbreeding resulting from population decline and fragmentation. The Iberian lynx (Lynx pardinus) provides a paradigmatic example of a species at the verge of extinction and, because of the well-documented and different demographic histories of the two remaining populations (Doñana and Andújar), it provides the opportunity to evaluate the performance of analytical methods that are commonly applied to detect genetic signatures of demographic decline. We used mitochondrial sequences and a set of 36 microsatellite markers to evaluate the current genetic status of the species and to assess the genetic signatures of its past history. Mitochondrial diversity was extremely low with only two haplotypes, alternatively fixed in each population. Both remnant populations have low levels of genetic diversity at microsatellite markers, particularly the population from Doñana, which has been isolated and at small census sizes at least since the 1950s, and genetic differentiation between the two populations is high. Bayesian coalescent-based methods suggest an earlier decline starting hundreds of years ago, while heterozygosity-excess and M-ratio tests did not provide conclusive and consistent evidence for recent population size changes. Also, a model of gene-flow received overwhelming support over a model of pure drift. The discrepancies observed between some of our results and the known recent history of the species call for caution in the interpretation of the outcomes of some of these methods, especially when no information on previous demographic history is available. Overall, our results suggest that current genetic patterns in the Iberian lynx are mainly the result of its recent decline and fragmentation and alerts on possible genetic risks for its persistence. Conservation strategies should explicitly consider this threat and incorporate an integrated genetic management of captive, wild and reintroduced populations, including the genetic restoration of wild populations through translocations.