BackgroundMycale ceciliais an abundant Eastern Tropical Pacific sponge living in a wide variety of habitats, including coral reefs where it may directly interact with corals. It is also known to possess secondary metabolites of pharmacological value. These aspects highlight the importance of having a better understanding of its biology, and genetic and population diversity.Methods and resultsIn the present study, we isolated and characterized twelve novel microsatellite loci by Illumina MiSeq sequencing. The loci were tested in 30 specimens collected from two coral reef localities (La Paz, Baja California Sur and Isabel Island, Nayarit) from the Mexican Pacific using M13(-21) labeling. All loci were polymorphic, with two to nine alleles per locus. Expected heterozygosities varied from 0.616 to 0.901. Eleven loci were tested and successfully amplified inM. microsigmatosafrom the Gulf of Mexico.ConclusionHere we report the first microsatellite loci developed for a sponge species from the Eastern Pacific coast. These molecular markers will be used for population genetic studies ofM. cecilia, and potentially in other congeneric species; particularly in vulnerable marine areas that require protection, such as coral reefs.