Tetraena mongolica is an endangered species that originated from the Tethys Ocean, and is now endemic to the Eastern Alxa–Western Ordos area. In the recent decades, this species has constantly suffered from environment deterioration and interference of human activities, thus leading to the habitat severely destructed and even disappeared. Rare information of molecular markers has limited the knowledge and protection for this germplasm. In the present study, we sequenced and assembled the transcriptome of T. mongolica, and obtained a dataset that contains 119603 transcribed sequences of the species. Among the assembled transcripts, 25721 Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) were detected from 21065 Unigenes, with the occurrence frequency of 21.51%. The most abundant motifs type of mononucleotide, dinucleotide, and trinucleotide were A/T, AG/CT, and ATC/ATG, respectively. Of the 39 SSR selected loci, 32 could amplify a total of 140 alleles in 48 individuals. The observed heterozygosity (Ho) ranged from 0.167 to 0.792 and the expected heterozygosity (He) from 0.252 to 0.789, with mean values of 0.462 and 0.579, respectively. The polymorphism information content (PIC) value ranged from 0.218 to 0.746, with an average value of 0.518. Collectively, SSR markers developed in this study might be useful to analyze the genetic structure and adaptive evolutionary mechanisms of T. mongolica, and lay a foundation for conservation, development, and utilization of the germplasm.