• Premise of the study: Corallodiscus is widespread across China and in adjacent countries to the west and south, with C. lanuginosus covering the entire range of the genus. Microsatellite markers will be useful to address within‐complex taxonomic and biogeographic structures of this species.
• Methods and Results: Fourteen markers were developed using the Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) protocol. Polymorphism was assessed in 12 individuals each from two populations from West Yunnan, China. Nine primers displayed polymorphisms. The number of alleles per locus ranged from one to six (mean: 2.7). The observed and expected heterozygosities ranged from 0 to 1 and from 0 to 0.772 (average: 0.487 and 0.448). Only one of the polymorphic loci deviated from Hardy–Weinberg equilibrium. Among the four congeneric species, cross‐amplification success ranged from two to eight markers.
• Conclusions: The markers will be useful for population genetic and evolutionary history studies for C. lanuginosus and the allied species C. bhutanicus, C. cooperi, and C. kingianus.