Abstract: SSR and SNP of Trichiurus japanicus were screened and analyzed respectively by MISA software,Samtools and GATK,basing on the transcriptome sequencing data of Trichiurus japanicus.Results showed the total number of SSRs were 49 311,including 44 625 complete microsatellites.The number of composite SSRs were 4 687.The size of SSR segment ranged from 11 to 374.There were 30 997 sequences with repetition length less than 20 bp.Among them,there were 7 523 SSRs with length between 12 and 20 bp,accounting for about 29.35% of the total number,showing medium polymorphism.And 13 627 long sequences with repetition length greater than 20 bp,accounting for about 53.18% of the total number,showing high polymorphism.A total of 876 199 SNP bits were obtained,including 335 218 transversals,540 981 transversals,and the ratio of transversals to transversals was 1.61:1.The number of SNPs in the non-coding region was 578 020.There were a total of 298 179 SNPs in the coding area.Among the base conversion types in the coding area,"C" to "T" accounted for the highest proportion,which was 22.09%.In addition,10 pairs of original primers of SSR and SNP were respectively provided in this study.This study could provide important scientific basis for the development of molecular markers,the construction of genetic linkage map and the protection of germplasm resources in the future.