Transcriptome analyses of Saxifraga sinomontana and Saxifraga consanguinea were carried out by Illumina HiSeq^TM 2000, then the characteristics of SSR and SNP were generalized according to the sequences. The result indicated that: 4 622 SSR sites were identified among 63 763 Unigenes with the frequency of 7.25% in S. sinomontana, there were 110 repeat motifs and the density of SSRs was 1/10.00 kb; for S. consanguinea, 4 542 SSRs were distributed in 60 972 Unigenes which accounted for 7.45%, there were 85 kinds of repeat motifs and SSRs occurred every 10.40 kb in length, which was slightly lower than that of S. sinomontana. For the two species, the trinucleotide was dominant repeat motif. The repeat numbers of SSRs were mainly from 5 to 10 and their motif length mainly ranged from 12-30 bp, which suggested that these SSRs displayed high levels of polymorphism. Besides, there were 118 424 and 112 006 SNPs in S. sinomontana and S. consanguinea. The proportion of SNPs in the coding region were 30.40% and 28.59% respectively, and the proportion of the synonymous mutations in the coding region (30.27%, 28.48%) was significantly higher than that of the nonsynonymous mutations (0.13%, 0.11%). It was found that the relevant indicators of the two species showed no significant difference, which was probably related to the tissue and its development stage, as well as the phylogenetic relationships of the species.