Abstract:Chloroplasts are the photosynthetic organ of green plants.The complete sequences of the chloroplast genomes of flowering plants have provided fresh impetus to phylogenetic reconstruction and evolution of flowering plants.Recently the number of the completely sequenced chloroplast genomes increased sharply and the advances in chloroplast genome evolution have revolutionized our understanding of the structural mutations and reorganizations of the chloroplast genomes.This paper summarized the recent discoveries of the structural diversity of the chloroplast genomes of flowering plants.Due to the emphases of chloroplast genome sequencing on the systematically key node species,genomic data of many major taxonomic groups are still unavailable.Such gaps need to be bridged for a better understanding the evolution of both the chloroplast genomes and the flowering plants.