Jute (Corchorus spp.) is a member of the Malvaceae family, which comprises more than 100 species. The systematic positions of jute species have remained unsettled. Chloroplasts are maternally inherited and their genomes are widely used for plant phylogenetic studies. In the present study, the chloroplast genomes of Corchorus capsularis and C. olitorius were assembled, with sizes of respectively 161,088 and 161,766 bp. Both genomes contained 112 unique genes (78 protein-coding, four rRNA, and 30 tRNA genes). Four regions with high variation between the two species were located in single-copy rather than inverted-repeat regions. A total of 66 simple sequence repeats (SSRs) were identified in the C. capsularis chloroplast genome and 56 in that of C. olitorius. Comparison of the two chloroplast genome sequences permitted the evaluation of nucleotide variation including 2417 single-nucleotide polymorphisms sites and 294 insertion or deletion sites, of which one marker (cpInDel 205) could discriminate the two jute species. Comparison of the C. capsularis and C. olitorius chloroplast genomes with those of other species in the Malvaceae revealed breakpoints in the accD locus, which is involved in fatty acid synthesis, in C. capsularis and C. olitorius. This finding suggests that genes from the chloroplast genome might have been transferred to the nuclear genome in some Corchorus species. This hypothesis was supported by synteny analysis of the accD region among the nuclear, chloroplast, and mitochondrial genomes. To our knowledge, this is the first report of the assembled chloroplast genome sequences of C. capsularis and C. olitorius. C. capsularis and C. olitorius are closely related to Gossypium species and there are abundant microstructure variations between these two genera. These results will expand our understanding of the systematics of species in the Malvaceae.