Complete chloroplast genome of Indonesian rare and endangered plants are still scarce, including those of Mangifera spp. This plant genus is economically important fruit. Bogor Botanical Garden in Indonesia is cultivating endangered Mangifera spp. listed in the IUCN redlist, including: Mangifera macrocarpa Blume, Mangifera pajang Kosterm., Mangifera pedicellata Kosterm., Mangifera rufocostata Kosterm., and Mangifera similis Blume. These plant spesies have no genomic resources available yet. Here, we generated paired-end short reads next-generation sequencing (NGS) data using Illumina Platform. The raw reads mainly will be assembled into complete chloroplast genome sequences. The results may lay foundation for further genomic studies which will be beneficial in their conservation efforts and sustainable utilizations.