Abstract:Several foliage horticultural varieties have been bred based on Spiraea × vanhouttei, including ‘Pink Ice’ and ‘Gold Fountain’, which exhibit excellent horticultural traits. However, the underlying mechanism of these two colorful leaf varieties remain poorly understood. To address this knowledge gap, the complete chloroplast genomes of ‘Pink Ice’ and ‘Gold Fountain’ were assembled by using genome skimming sequencing. Comparative genomic analysis of all available chloroplast genomes of the genus Spiraea to date was studied, including variation hotspot analysis, simple repetitive sequence analysis, and phylogenetic analysis. The results showed that both varieties had a typical quadripartite structure, consisting of one LSC, one SSC, and two IRs. The chloroplast genomes of ‘Pink Ice’ and ‘Gold Fountain’ were 155 953 and 155 941 bp in size, respectively, and each contains 130 genes, including 85 protein-coding genes, 37 transfer RNA genes and 8 ribosomal RNA genes. The two chloroplast genomes also contained 67 and 69 simple repetitive sequences, respectively, with single nucleotide repeat sequences being the most abundant. There were seven highly variable regions within these two chloroplast genomes, including trnH_GUG-psbA, trnK_UUU, trnR_UCU-atpA, trnT_GCU-psbD, ndhC, rpl32, and ycf1. Finally, phylogenetic analysis revealed that ‘Pink Ice’ and ‘Gold Fountain’ could not be considered a monophyletic group, despite their close relationship. Overall, these would provide valuable insights into the chloroplast genomes of two foliage varieties of Spiraea, which would aid in the development of more horticultural resources for this genus in the future.