BACKGROUND: Camellia reticulata Lindl. (C. reticulata) is the tallest ornamental camellia globally, with wild populations comprising a polyploid complex of diploids (2×), tetraploids (4×), and hexaploids (6×). The type specimen of C. reticulata is a heteroploid hexaploid derived from 2 × ancestors, including C. pitardii, C. saluenensis, and 2 × C. reticulata. Currently, limited information exists regarding the evolutionary characteristics of the chloroplast genomes of C. reticulata at different ploidy levels, and the phylogenetic position of 2 × and 4 × C. reticulata remains unclear. RESULTS: This study sequenced, assembled, and annotated the chloroplast genomes of 2 × and 4 × C. reticulata, comparing them with those of 6 × C. reticulata and other closely related species. The results indicated that the chloroplast genome sizes of C. reticulata ranged from 156,519 to 156,927 bp, with gene counts, distributions, GC content, and codon usage being similar across different ploidy levels. The ycf1 gene exhibited significant differentiation among species, and was identified as a candidate for adaptive evolution in C. reticulata. Additionally, 11 highly differentiated intergenic regions were identified, with six hotspots of variation that can serve as molecular markers for genetic studies in C. reticulata populations. Analysis of selection pressure indicated that four genes were under positive selection. Phylogenetic analysis revealed that the polyploid complex of C. reticulata, along with C. pitardii, C. saluenensis, and C. mairei, formed a well-supported clade. The genetic distances between 6 × C. reticulata and its three 2 × ancestors were relatively small. CONCLUSION: Camellia pitardii, C. saluenensis, and C. mairei may have participated in the allopolyploidization of C. reticulata, with both 2 × and 4 × C. reticulata have the potential for independent classification. These findings provide valuable insights into chloroplast genome alterations following allopolyploidization, establishing a crucial foundation for understanding the systematic evolutionary history of various ploidy levels in C. reticulata.