Premise of the study:Bombax ceiba (Malvaceae), commonly known as silk cotton tree, is a multipurpose tree species of tropical forests. Novel expressed sequence tag–simple sequence repeat (EST‐SSR) markers were developed and characterized for the species using transcriptome analysis.Methods and Results:A total of 33 new EST‐SSR markers were developed for B. ceiba, of which 13 showed polymorphisms across the 24 individuals from four distant populations tested in the study. The results showed that the number of alleles per polymorphic locus ranged from two to four, and the expected heterozygosity and observed heterozygosity per locus varied from 0.043 to 0.654 and from 0 to 0.609, respectively.Conclusions:These newly developed EST‐SSR markers can be used in phylogeographic and population genetic studies to investigate the origin of B. ceiba populations. Furthermore, these EST‐SSR markers could also greatly promote the development of molecular breeding studies pertaining to silk cotton tree.