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Paraisometrum mileense is a unique species of Paraisometrum endemic to south-west China, which is a “100-years-lost” plant and was rediscovered in 2006. In this paper, complete plastid genome of P. mileense is firstly assembled and characterized. The length of total plastid genome is 153,259 bp consisting of a large single-copy region (LSC) of 84,293 bp, a small single-copy region (SSC) of 18,162 bp, and two inverted repeat regions (IRs) of 25,402 bp. In total, 113 genes are predicted, including 80 protein-coding genes (PCGs), four rRNA genes and 29 tRNA genes. Phylogenetic analysis indicated that P. mileense with the other eight Gesneriaceae species formed a clade with a 100% bootstrap support.