Abstract
Cupressus funebris Endl., a widely cultivated evergreen species in China, plays important ecological and economic roles in afforestation, ecological restoration, and the production of essential oils and medicinal compounds. However, its phylogenetic position and taxonomic status within Cupressaceae has long been debated. In this study, we sequenced and annotated the complete chloroplast genome of C. funebris and performed comparative analyses using nine additional Cupressaceae species as references to place C. funebris in a broader evolutionary context. The genome of C. funebris is 127,816 bp in length and encodes 117 genes. Comparative analyses indicated that the chloroplast genome structure of C. funebris is highly conserved relative to other Cupressaceae species, while sequence divergence was mainly concentrated in several genes, including accD, ycf1, ycf2, and rpoC2. Codon usage analysis of C. funebris revealed a clear bias toward codons ending in A or U. In addition, a total of 709 simple sequence repeats (SSRs) identified from comparative analyses provided potential molecular markers relevant to genetic studies of C. funebris. Phylogenetic analysis based on 65 complete chloroplast genomes further clarified the evolutionary placement of C. funebris within Cupressaceae and yield relationships largely consistent with traditional taxonomy. Notably, SNP-rich regions within the rpoA and rpoC2 genes were identified as informative loci for distinguishing C. funebris from closely related taxa. Overall, this study provides a comprehensive chloroplast genomic resource for C. funebris and contributes to a better understanding of its evolutionary position and taxonomic relationships within Cupressaceae. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12660-8.