Genome-wide identification of simple sequence repeats and assessment of genetic diversity in Hedychium

•Identified 266,825 SSR loci with 273 motif types of Hedychium ‘ZS’ genome sequence.•Mono- and Di-nucleotide repeats are the most abundant repeat types accounted for 87.14 % of all the SSRs identified.•Genetic structure and PCoA analysis grouped 44 Hedychium accessions into cultivated and wild genotypes using 22 screened genomic SSR primers.