Abstract: 【Objective】By analyzing the whole genome data of Litsea cubeba，SSR molecular markers were developed and the SSR-PCR reaction system was optimized，which provided reference for studying the genetic diversity of Litsea cubeba germplasm resources，molecular marker-assisted breeding and constructing core germplasms.【Methods】 Based on the whole genome sequence of Litsea cubeba，the SSR loci were mined by MISA（1.0），and their characteristics were analyzed，and the correlation of SSR numbers of different repeat types in the whole genome of Litsea cubeba was analyzed. The SSR-PCR reaction system of Litsea cubeba was optimized by orthogonal test with 4 factors and 3 levels.【Result】A total of 303202 SSR markers were detected in the whole genome of Litsea cubeba，with an average length of 25.95 bp. The total length of Litsea cubeba genome was 1.3 Gb，the longest was chromosome 1，and the shortest was chromosome 12，which were 161.20 Mb and 55.35 Mb respectively. There were 259695 complete nucleotide SSR on chromosomes，with the highest richness in mononucleotide and the lowest richness in hexanucleotide，among which 202278 SSR≤20 bp（77.89%），and the frequency density of SSR loci on each chromosome was 172-231 locus/Mb. Among the 12 pairs of chromosomes in Litsea cubeba，the number of SSR on chromosome 2 was the largest，accounting for 36366（14.00%），and the number of SSR on chromosome 12 was the least，accounting for 9499（3.66%）. There were 4471 and 2091 different repeat types and different repeat motif types of complete nucleotide，262，459，494，543，1011 and 1702 different repeat types of mononucleotide to hexanucleotide，and 4，12，60，219，586 and 1210 different repeat motif types respectively，and the dominant repeat unit was T，AT，AAT，AAAT，TTGGT and TGTATT，showing an obvious A/T base preference. The repeat frequency of different SSR types ranged from 4 to 240，and the number of SSR loci distributed from 4 to 10 was the largest，totaling 134725（51.88%）. The frequency of repeated motifs in different chromosomes was mainly concentrated from 4 to 20. The correlation analysis of the number of SSR of different repeat types in the whole genome of Litsea cubeba showed that there was extremely significant positive correlation between SSR loci of different repeat types（P<0.01），and the correlation coefficient of mononucleotide and dinucleotide was the largest（0.997）. Under the orthogonal test，the number 5 band was clear and bright，which was the best band.【Conclusion】The number and types of SSR in Litsea cubeba genome are abundant，and there is obvious A/T base preference. The optimum combination of SSR-PCR reaction system of Litsea cubeba is as follows：DNA template concentration 50 ng/μL，primer amount 1.5 μL，annealing temperature 60 ℃ and 28 cycles.