BackgroundCuscuta, a parasitic plant species in the Convolvulaceae family, grows in many countries and regions. However, the relationship between some species is still unclear. Therefore, more studies are needed to assess the variation of the chloroplast (cp) genome inCuscutaspecies and their relationship with subgenera or sections, thus, providing important information on the evolution ofCuscutaspecies.ResultsIn the present study, we identified the whole cp genomes ofC. epithymum,C. europaea,C. gronovii,C. chinensisandC. japonica, and then constructed a phylogenetic tree of 23Cuscutaspecies based on the complete genome sequences and protein-coding genes. The complete cp genome sequences ofC. epithymumandC. europaeawere 96,292 and 97,661 bp long, respectively, and lacked an inverted repeat region. Most cp genomes ofCuscutaspp. have tetragonal and circular structures except forC. epithymum,C. europaea, C. pedicellataandC. approximata. Based on the number of genes and the structure of cp genome and the patterns of gene reduction, we found thatC. epithymumandC. europaeabelonged to subgenusCuscuta. Most of the cp genomes of the 23Cuscutaspecies had single nucleotide repeats of A and T. The inverted repeat region boundaries among species were similar in the same subgenera. Several cp genes were lost. In addition, the numbers and types of the lost genes in the same subgenus were similar. Most of the lost genes were related to photosynthesis (ndh,rpo,psa,psb,pet, andrbcL), which could have gradually caused the plants to lose the ability to photosynthesize.ConclusionOur results enrich the data on cp. genomes of genusCuscuta. This study provides new insights into understanding the phylogenetic relationships and variations in the cp genome ofCuscutaspecies.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-023-09427-w.