Abstract: Zea, commonly known as the maize, includes Zea mays, commonly known as maize,and its wild relatives. It is not only one of the globally important cereals but also a model plant for basic research. This study used NCBI’s published Illumina second-generation sequencing data of 201 Zea mays L. plants to comprehensively explore the chloroplast genomes of yucca plants by assembling,annotating and analysing them. The results showed the chloroplast genomes of Zea species exhibit a typical circular tetrad structure, with a length ranging from 140 443 to 141 050 bp, with a GC content of38.4%, and a total of 128 genes were annotated; RSCU analysis revealed significant differences between maize and other species, particularly in the preference for the UUA codon; overall, there were no significant differences in repetitive sequences between maize and other species, but there were substantial differences in simple repeat sequence types; all the samples were divided into four groups in the phylogenetic analysis, identifying a total of 79 haplotypes, with samples from the same group clustering together, and principal component analysis results supporting clear separation of samples from different groups; nucleotide polymorphism analysis accurately identified 10 highly variable sites that could serve as potential DNA barcodes. In summary, this study elucidated the genetic variation and systematic evolution among the chloroplast genomes of 201 Zea species, providing a new perspective on organelle genetic genomes to accelerate maize breeding processes.