Abstract The plant species Cedrela odorata has been largely exploited in the timber industry due to the high demand of its wood. Therefore, C. odorata , has been considered as a vulnerable species since 1994, with the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). C. odorata is one of the key timber species included in the management and conservation plans in Colombia. These plans include the study of local populations by developing genetic resources for the species. In this study, two novel chloroplast (cp) genomes have been generated using the MinION long read sequencing technology. The new cp assemblies were compared with other cp genomes for the species, supporting previous hypothesis of intraspecific diversity associated to their place of origin. Furthermore, the cp genomes were screened for sequence variants (SV) and a total of 16 SNPs were identified, presumably unique to populations of the amazon region in Colombia. Here, the first cp genome sequences of C. odorata from Colombian individuals represent novel and valuable genomic resources for the species suitable for DNA fingerprinting and DNA barcoding applications.