• Premise of the study: This work aimed to develop microsatellite markers for Cratylia mollis as tools to assess its genetic diversity and structure and to evaluate their potential cross‐amplification in related species.• Methods and Results: Microsatellite markers were developed using a microsatellite‐enriched library and an intersimple sequence repeat library. From a set of 19 markers, 12 microsatellite loci were polymorphic and presented considerable variation in allele number (2–11), expected heterozygosity (0.226–0.883), and polymorphism information content per locus (0.212–0.870). Cross‐amplification in C. argentea was successful in 16 loci, 12 of which were polymorphic (2–10 alleles).• Conclusions: The polymorphism of this set of microsatellite markers for C. mollis, as well as their successful cross‐amplification in C. intermedia and C. bahiensis and their transferability to C. argentea, supports their use in future comparative studies to understand the mechanism involved in population divergence and speciation in the genus.