The genomes and chromosomes of the important fibre crops white jute and Tossa jute (Corchorus species) are poorly characterized. Information is essential for breeding and improvement, with characters including environmental adaptability, fibre quality and susceptibility to diseases differing between the species. Begum et al. use a comparative analysis of a prominent satelllite DNA family, identified in this study, to reveal its diversification and emerging subfamily structure in both jute genomes, while the heterogenous distribution along chromosomes is conserved. In combination with ribosomal genes and retrotransposon sequences, they use the chromosome-specific distribution of the satellite DNA for in situ hybridization to generate a reference karyotype for both jute species. These sequences and data will be useful for genetic mapping and analysis of hybrid lines.