Abstract: To develop co-dominant microsatellite molecular markers (SSRs) for studying conservation genetics of the giant lobelia endemic to east Africa, we sequenced the genome of the giant lobelia, Lobelia deckenii, using next-generation high-throughput sequencing technology. Using the MISA program, we acquired a total of 58966 SSRs, from which we designed 3558 SSR primer pairs using Primer software. We selected 40 primer pairs at random to evaluate their application across six individuals from three L.deckenii populations (two individuals per population). Thirty-two markers were successfully amplified, yielding clear and discernible bands. Using 24 L.deckenii individuals from the Mountain Kenya population, we tested the polymorphism of the 32 SSR markers and found that 14 were polymorphic. Using these 14 polymorphic SSR markers, we detected a total of 86 alleles. The number of alleles per locus ranged from four to nine. Observed heterozygosity (H_o) and expected value (H_e) per locus varied from 0.000 to 1.000 and 0.625 to 0.854, respectively. Our results indicated that development of SSR markers from genomic data by high-throughput sequencing in the giant lobelia was valuable and effective. These newly generated SSR markers will provide novel tools for studying genetic diversity, population genetic structure and conservation biology of giant lobelias in east Africa.