Premise of the study: Microsatellite primers were designed for the submersed aquatic plant Cabomba aquatica s.l. (Cabombaceae) and characterized to estimate genetic diversity parameters. Methods and Results: Using a selective hybridization method, we designed and tested 30 simple sequence repeat loci using two natural populations of C. aquatica s.l., resulting in 13 amplifiable loci. Twelve loci were polymorphic, and alleles per locus ranged from two to four across the 49 C. aquatica s.l. individuals. Observed heterozygosity, expected heterozygosity, and fixation index varied from 0.0 to 1.0, 0.0 to 0.5, and-1.0 to-0.0667, respectively, for the Manaus population and from 0.0 to 1.0, 0.0 to 0.6, and-1.0 to 0.4643 for the Viruá population. Conclusions: The developed markers will be used in further taxonomic and population studies within Cabomba. This set of microsatellite primers represents the first report on rapid molecular markers in the genus. © 2015 Barbosa et al.311 Billotte, N., Lagoda, P.J.L., Risterucci, A.M., Baurens, F.C., Microsatellite-enriched libraries: Applied methodology for the development of SSR markers in tropical crops (1999) Fruits, 54, pp. 277-288Creste, S., Tulmann Neto, A., Figueira, A., Detection of single sequence repeat polymorphisms in denaturing polyacrylamide sequencing gels by silver staining (2001) Plant Molecular Biology Reporter, 19, pp. 299-306Doyle, J.J., Doyle, J.L., A rapid DNA isolation procedure from small quantities of fresh leaf tissue (1987) Phytochemical Bulletin, 19, pp. 11-15Esteves, F.A., (1998) Fundamentos de Limnologia. Interciência/FINEP, , Rio de Janeiro, BrazilFassett, N.C., A monograph of Cabomba (1953) Castanea, 13, pp. 116-128Francisco, L.V., Barreto, R.C., Cabomba aubl. (Cabombaceae): Caracterizacąõ morfoecológica e delimitacąõ entre as espécies ocorrentes no Brasil (2007) Revista Brasileira de Biociências, 5, pp. 1077-1079Goudet, J., HIERFSTAT, a package for R to compute and test hierarchical F-statistics (2005) Molecular Ecology Notes, 5, pp. 184-186Orgaard, M., The genus Cabomba (Cabombaceae): A taxonomic study (1991) N Ordic Journal of Botany, 11, pp. 179-203Raymond, M., Rousset, F., GENEPOP (version 1.2): Population genetics software for exact tests and ecumenism (1995) Journal of Heredity, 86, pp. 248-249Silva, J.B.A., Leite, V.L., Reproductive biology and pollination of Cabomba aquatica (Cabombaceae) (2011) Rodriguésia, 62, pp. 919-926Untergasser, A., Nijveen, H., Rao, X., Bisseling, T.T., Geurts, R., Leunissen, J.A.M., Primer3Plus, an enhanced web interface to Primer3 (2007) N Ucleic Acids Research, 35, pp. W71-W74