We describe the development and characterisation of six new dinucleotide motif microsatellite loci for populations of marine iguanas (Amblyrhynchus cristatus), endemic to the Galapagos archipelago. Primers were based on microsatellite-bearing sequences and initially developed using universally labelled primers. When analysed across 5 populations (representing 150 individuals), new loci displayed, on average, high levels of genetic diversity (range: 2-13 alleles, mean: 5.73) and values of heterozygosity (range: 0.0-0.906, mean: 0.605). No consistent deviations from Hardy-Weinberg equilibrium or significant linkage disequilibrium were observed, and all loci were shown to be free of common microsatellite errors. Utilising the 13 previously available microsatellite loci for this species, we describe here four multiplex combinations for the successful amplification of 19 microsatellite loci for marine iguanas. This powerful set of highly polymorphic markers will allow researchers to explore future questions regarding the ecology, evolution, and conservation of this unique species.