The genusHoupoeabelongs to the family Magnoliaceae, and the species in this genus have important medicinal values. However, the investigation of the correlation between the evolution of the genus and its phylogeny has been severely hampered by the unknown range of species within the genus and the paucity of research on its chloroplast genome. Thus, we selected three species ofHoupoea:Houpoea officinalisvarofficinalis(OO),Houpoea officinalisvar. biloba(OB), andHoupoea rostrata(R). With lengths of 160,153 bp (OO), 160,011 bp (OB), and 160,070 bp (R), respectively, the whole chloroplast genomes (CPGs) of these threeHoupoeaplants were acquired via Illumina sequencing technology, and the findings were annotated and evaluated. These three chloroplast genomes were revealed by the annotation findings to be typical tetrads. A total of 131, 132, and 120 different genes were annotated. The CPGs of the three species had 52, 47, and 56 repeat sequences, which were primarily found in the ycf2 gene. A useful tool for identifying species is the approximately 170 simple sequence repeats (SSRs) that have been found. The border area of the reverse repetition region (IR) was studied, and it was shown that across the threeHoupoeaplants, it is highly conservative, with only changes betweenH. rostrataand the other two plants observed. Numerous highly variable areas (rps3-rps19, rpl32-trnL, ycf1, ccsA, etc.) have the potential to serve as the barcode label forHoupoea, according to an examination of mVISTA and nucleotide diversity (Pi). Phylogenetic relation indicates thatHoupoeais a monophyletic taxon, and its genus range and systematic position are consistent with the Magnoliaceae system of Sima Yongkang-Lu Shugang, including five species and varieties ofH. officinalisvar.officinalis,H. rostrata,H. officinalis var. biloba,Houpoea obovate, andHoupoea tripetala, which evolved and differentiated from the ancestors ofHoupoeato the presentHoupoeain the above order. This study provides valuable information on the genusHoupoea, enriches the CPG information onHoupoeagenus, and provides genetic resources for the further classification of and phylogenetic research onHoupoea.