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Agave species are an important family of crassulacean acid metabolism (CAM) plants with remarkable tolerance to heat and drought stresses (Agave deserti) in arid regions and multiple agricultural applications, such as spirit (Agave tequilana) and fiber (Agave sisalana) production. However, the systematic position and phylogenetic relationship of agave species still remain ambiguous at chloroplast genome level. We hence reviewed recent advances in published complete chloroplast genomes of agave species, with the aim to reveal their phylogenetic relationship at chloroplast genome level. This book will benefit future studies related to chloroplast genomes in Agave genus.