Corchorus capsularis(white jute) and C. olitorius(dark jute) are the two principal cultivated spedes of jute that produce natural bast fiber of commercial importance. We have identified 4509 simple sequence repeat(SSR) loci from 34,163 unigene sequences of C. capsularis to develop a non-redundant set of 2079 flanking primer pairs. Among the SSRs, trinudeotide repeats were most frequent(60%) followed by dinucleotide repeats(37.6%). Annotation of the SSR-containing unigenes revealed their putative functions in various biological and molecular processes, including responses to biotic and abiotic signals. Eighteen expressed gene-derived SSR(eSSR) markers were successfully mapped to the existing single-nucleotide polymorphism(SNP) linkage map of jute,providing additional anchor points. Amplification of 72% of the 74 randomly selected primer pairs was successful in a panel of 24 jute accessions, comprising five and twelve accessions of C.capsularis and C. olitorius, respectively, and seven wild jute spedes. Forty-three primer pairs produced an average of 2.7 alleles and 58.1% polymorphism in a panel of 24 jute accessions. The mean PIC value was 0.34 but some markers showed PIC values higher than 0.5, suggesting that these markers can efficiently measure genetic diversity and serve for mapping of quantitative trait loci(QTLs) in jute. A primer polymorphism survey with parents of a wide-hybridized population between a cultivated jute and its wild relative revealed their efficacy for interspecific hybrid identificatioii. For ready accessibility of jute eSSR primers, we compiled all information in a user-friendly web database, JuteMarkerdb(http://jutemarkerdb.icar.gov.in/) for the first time in jute.This eSSR resource in jute is expected to be of use in characterization of germplasm, interspecific hybrid and variety identification, and marker-assisted breeding of superior-quality jute. Corchorus capsularis (white jute) and C. olitorius (dark jute) are the two principal cultivated spedes of jute that produce natural bast fiber of commercial importance. We have identified 4509 simple sequence repeat (SSR) loci from 34,163 unigene sequences of C. capsularis To develop a non-redundant set of 2079 flanking primer pairs. Among the SSRs, trinudeotide repeats were most frequent (60%) followed by dinucleotide repeats (37.6%). Annotation of the SSR-containing unigenes revealed their putative functions in various biological and Molecular processes, including responses to biotic and abiotic signals. Eighteen expressed gene-derived SSR (eSSR) markers were successfully mapped to the existing single-nucleotide polymorphism (SNP) linkage map of jute, providing additional anchor points. 74 randomly selected primer pairs were successful in a panel of 24 jute accesions, including five and twelve accessions of C. capsularis and C. olitorius, respectively, and seven w mean jute spedes. Forty-three primer pairs produced an average of 2.7 alleles and 58.1% polymorphism in a panel of 24 jute accesions. The mean PIC value was 0.34 but some markers showed PIC values ​​higher than 0.5, suggesting that these markers canfficient measure genetic diversity and serve for mapping of quantitative trait loci (jTLs) in jute. A primer polymorphism survey with parents of a wide-hybridized population between a cultivated jute and its wild relative reveals their efficacy for interspecific hybrid identificatioii. For ready accessibility of jute eSSR primers, we compiled all information in a user-friendly web database, JuteMarkerdb (http://jutemarkerdb.icar.gov.in/) for the first time in jute.This eSSR resource in jute is expected to be of use in characterization of germplasm, interspecific hybrid and variety identification, and marker-assisted breeding of superior-quality jute.