We studied patterns of genetic diversity within and among 5 populations (318 individuals) of Galápagos marine iguanas (Amblyrhynchus cristatus) from the island Santa Fé. Populations were separated by distances of 0.2 to 9.9 km. We sequenced 1182 base pairs of the mitochondrial control region and screened 13 microsatellite loci for variability. We also added data from 5 populations (397 individuals) sampled on 4 neighboring islands (Santa Cruz, Floreana, Espanola, and San Cristobal). The 5 Santa Fé populations, revealed as genetically distinct from populations on other islands, present relatively low levels of genetic diversity, which are similar for both microsatellite (average observed heterozygosity from 0.7686 to 0.7773) and mitochondrial DNA (mtDNA) markers (haplotypic and nucleotide diversity from 0.587 to 0.728 and from 0.00079 to 0.00293, respectively), and comparable with those observed in similar-sized sampling sites on other islands. There was frequency-based evidence of genetic structure between northern and southern sites on Santa Fé (F(st) of 0.0027-0.0115 for microsatellite and 0.0447-0.2391 for mtDNA), but the 4 southern sites showed little differentiation. Most of the intra-island genetic variation was allocated within rather than between sites. There was no evidence of sex-biased dispersal or population substructuring due to lek-mating behavior, suggesting that these 2 observed behaviors are not strong enough to leave an evolutionary signal on genetic patterns in this species.