Genetic variability is an important component in the ability of populations to adapt in the face of environmental change. Here we report the first description of nuclear genetic variability in the only remaining sizable colony of the Mediterranean monk seal (Monachus monachus), located at Cap Blanc (Western Sahara, Mauritania), whose estimated size during the study period (1994–May 1997) was about 320 individuals. We tested 42 microsatellite loci isolated from five pinniped species in a sample of 52 pups. Three loci failed to give any product, and of the remaining 39, only 15 were polymorphic, with a maximum of 3 alleles detected. Three loci appeared to be X-linked. No departures from Hardy-Weinberg equilibrium were detected and no genetic structure was found between the two nursing caves currently occupied by the seals. Several analytical methods show that, as a consequence of a severe bottleneck, the population has suffered a decrease in genetic variability over the last few centuries.