Abstract: In order to understand the detailed information of SSR and SNP molecular markers in the transcriptome of Azolla imbircata under different nitrogen concentration stress, the SSR and SNP loci distributed in the transcriptomic data were analyzed. By extracting RNA from the roots and leaves of Azolla imbircata, the cDNA library was constructed and the high-throughput sequencing was performed using the next generation sequencing platform. The SSR characteristics of the sequencing data were analyzed using MISA, and the software STAR was used for the comparison and the SNP identification was performed by GATK. The results showed that: there were a total of 9009 SSR loci in the transctiptome group of Azolla imbircata, and the frequency of SSR loci was 30.12%. Among them, the trinucleotide and mononucleotide repeats were the two most SSR type, which accounted for 43.66% and 26.41% of the total repeats, respectively. There were 439217 SNP loci, including the conversion types (282532) and transversion types (156685). The proportion of conversion types (64.33%) was significantly higher than that of transversion types (35.67%). Among all the variation types, C/T had the highest proportion, accounting for 17.33% of the total SNP loci, followed by G/A with 17.01%. The transcription group of Azolla imbircata had abundant SSR and SNP loci, which could provide a basis for the study of genetic diversity and the genetic structure and differentiation, as well as the development and utilization of functional genes.