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Background   Pilea  is a genus of perennial herbs from the family Urticaceae, and some species are used as courtyard ornamentals or for medicinal purposes. At present, there is no information about the plastid genome of  Pilea , which limits our understanding of this genus. Here, we report 4 plastid genomes of  Pilea  taxa ( Pilea mollis ,  Pilea glauca  ‘Greizy’,  Pilea peperomioides  and  Pilea serpyllacea  ‘Globosa’) and performed comprehensive comparative analysis.    Results  The four plastid genomes all have a typical quartile structure. The lengths of the plastid genomes ranged from 150,398 bp to 152,327 bp, and each genome contained 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Comparative analysis showed a rather high level of sequence divergence in the four genomes. Moreover, eight hypervariable regions were identified ( pet N- psb M,  psb Z- trn G-GCC,  trn T-UGU- trn L-UAA,  acc D- psb I,  ndh F- rpl 32,  rpl 32- trn L-UAG,  ndh A-intron and  ycf 1), which are proposed for use as DNA barcode regions. Phylogenetic relationships based on the plastid genomes of 23 species of 14 genera of Urticaceae resulted in the placement of  Pilea  in the middle and lower part of the phylogenetic tree, with 100% bootstrap support within Urticaceae.    Conclusion  Our results enrich the resources concerning plastid genomes. Comparative plastome analysis provides insight into the interspecific diversity of the plastid genome of  Pilea . The identified hypervariable regions could be used for developing molecular markers applicable in various research areas.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-020-02793-7.

Comparative plastid genomics of four Pilea (Urticaceae) species: insight into interspecific plastid genome diversity in Pilea