Abstract: 【Objective】 The sequence features and phylogenetic evolutionary relationship of Wuyi Mingcong chloroplast genome were analyzed to strengthen the identification of germplasm and the development and utilization of resource diversity of Wuyi Mingcong.【Method】 Combined with PacBio and Illumina high-throughput sequencing, sequencing, assembly, and annotation of the complete chloroplast genomes of five representative Wuyi Mingcong varieties(Baijiguan, Bantianyao, Shuijingui, Rougui and Tieluohan) were conducted. In combination with the genome sequence of Dahongpao published, the sequence characteristics and phylogenetic analysis of the chloroplast genomes of six Wuyi Mingcongs were carried out.【Result】 Six chloroplast genomes of Wuyi Mingcong ranged between 157024 bp and 157126 bp in length, all were composed of circular, double-stranded DNA, including two reverse repeat regions(IR, 25944-26095 bp), one large single copy region(LSC, 86594-86859 bp) and one small single copy region(SSC, 18276-18291 bp). A total of 92 protein coding genes, 37 tRNAs, and 8 rRNAs were annotated. By comparison, 1276 simple repeat sequences(SSRs), 65 long repeat sequencesand 93 insertion-deletion(Indel) were identified. The chloroplast genomes of the six Wuyi Mingcong varieties showed highly similar codon preference, and the number of high frequency codons(RSCU>1) was 30, among which, the number of codons ending with A and U was the largest, with the strongest preference for UUA. In the phylogenetic tree based on chloroplast whole-genome, not all varieties of tea subgenus and Camellia subgenus were clustered into one branch, and six Wuyi Mingcong varieties were not clustered into one branch, among which Dahongpao and Rougui were closer to Longjing 43 branch, Bantianyao and Anhua tea were clustered into one branch, Shuijingui and Tieguanyin were clustered into one branch, and Baijiguan and Tieluohan each formed a single branch respectively.【Conclusion】 The chloroplast genomes of the six Wuyi Mingcong are similar in size, structure and codon preference, but have certain diversity. The chloroplast genome can be used as a super barcode for cultivar identification and population genetic research of Wuyi Mingcong.