The wild shaddock (Citrus maxima) has been an important species in the development of the fruit breeding program in the genus Citrus, family Rutaceae. However, the majority of its natural resources are subject to deforestation which, accompanied with the lack of efficient conservation efforts in recent decades, has severely shrunk its wild populations and threatened its germplasm resources. In this study, we determined and analyzed the complete chloroplast genome of wild shaddock. It was 160,133 bp in length, containing a pair of 26,845 bp inverted repeat regions (IRs) separated by one large and one small single copy region (SSC and LSC) of 88,043 and 18,400 bp, respectively. Phylogenetic analysis of all sequenced chloroplast genomes in the Rutaceae suggested that shaddock was closely related to three other Citrus species. This complete chloroplast genome will provide valuable information for the development of highly variable DNA markers for future population and conservation studies of wild shaddock.