BackgroundUlmus mianzhuensisis an endemic tree species in China with high ornamental and economic value. Currently, little is known regarding its genomic architecture, phylogenetic position, or adaptive evolution. Here, we sequenced the complete chloroplast genome (cp genome) ofU. mianzhuensisand further compared the variations in gene organization and structure withinUlmusspecies to define their genomic evolution, then reconstructed the phylogenomic relationship of 31 relatedUlmusspecies to explore the systematic position ofU. mianzhuensisand the utility of cp genome for resolving phylogenetics amongUlmusspecies.ResultsOur results revealed that all theUlmusspecies exhibited a typical quadripartite structure, with a large single copy (LSC) region of 87,170 − 88,408 bp, a small single copy (SSC) region of 18,650 − 19,038 bp and an inverted repeat (IR) region of 26,288 − 26,546 bp. WithinUlmusspecies, gene structure and content of cp genomes were highly conserved, although slight variations were found in the boundary of SC/IR regions. Moreover, genome-wide sliding window analysis uncovered the variability ofndhC-trnV-UAC,ndhF-rpl32, andpsbI-trnS-GCUwere higher among 31Ulmusthat may be useful for the population genetics and potential DNA barcodes. Two genes (rps15andatpF) were further detected under a positive selection ofUlmusspecies. Comparative phylogenetic analysis based on the cp genome and protein-coding genes revealed consistent topology thatU. mianzhuensisis a sister group toU. parvifolia(sect.Microptelea) with a relatively low-level nucleotide variation of the cp genome. Additionally, our analyses also found that the traditional taxonomic system of five sections inUlmusis not supported by the current phylogenomic topology with a nested evolutionary relationship between sections.ConclusionsFeatures of the cp genome length, GC content, organization, and gene order were highly conserved withinUlmus. Furthermore, molecular evidence from the low variation of the cp genome suggested thatU. mianzhuensisshould be merged intoU. parvifoliaand regarded as a subspecies ofU. parvifolia. Overall, we demonstrated that the cp genome provides valuable information for understanding the genetic variation and phylogenetic relationship inUlmus.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-023-09430-1.