Despite Salvia miltiorrhiza being one of the most important medicine plants in China, there is a limited availability of genomic resources, especially of the expressed sequence tag-based markers. In this study, we selected and characterized functional markers in S. miltiorrhiza, which consisted of 4,192 non-redundant expressed sequence tags (ESTs) from 10,288 identified S. miltiorrhiza ESTs in dbEST data bank. Among them, 159 simple sequence repeats (SSR) were detected, which amounted to 3.79% of the non-redundant starting sequence population. This incidence was equivalent to one EST-SSR in every 12.74 kb of S. miltiorrhiza ESTs. Among the different motifs ranging from 1 bp to 6 bp, di-nucleotide repeat motif was the most abundant (77, 48.43%), followed by tri-nucleotide (41, 25.79%), hexa-nucleotide (23, 14.47%), penta-nucleotide (12, 7.55%) and tetra-nucleotide (6, 3.77%). In 47 identified motif types, the detected frequency above 5% were GA/CT (16.35%), AG/TC (15.09%), TCA/AGT (10.69%), AT/TA (6.29%), GAAAAG/CAAAAC (6.29%) and TA/AT (5.03%). Based on flank sequence of detected SSR, a total of 83 EST-SSR primer pairs were designed and tested for the amplification efficiency, polymorphism and transferability in thirteen S. mihiorrhiza samples and other ten species from the genus Salvia. The results showed that 72 primer pairs were successfully amplified in S. miltiorrhiza samples to yield and 279 loci with an average of 3.88 loci per primer pair. The cross-transferability of S. miltiorrhiza EST-SSR markers to other ten Salvia plants was very high, ranging from 60% to 100% with an average of 85%. Further analysis of the genetic similarity based on the polymorphic bands showed the EST-SSR could detect the genetic diversity on different levels among the whole test samples and distinguish the S. miltiorrhiza from other Salvia plants effectively. It is expected that the potential markers described here would add to the repertoire of DNA markers needed for genetic analysis, linkage mapping and comparative genomics studies in S. miltiorrhiza and related Salvia genus plants.