Ten microsatellite loci were developed for the Baja California spiny-tailed iguana Ctenosaura hemilopha, using an enriched genomic DNA library. In the Cerralvo Island population, seven loci were polymorphic and presented moderate levels of variation. Number of alleles ranged from two to eight (average 4.43), and observed heterozygosity from 0.150 to 0.857 (average 0.492). Polymorphism was detected at six loci on C. hemilopha individuals from the southern Baja California Peninsula. These markers will be useful to study familiar relationships and behaviour on the Cerralvo Island population.