Phylogenetic analyses based on comparison of a limited number of genes recently suggested that Amborella trichopoda is the most ancient angiosperm. Here we present the complete sequence of the chloroplast genome of this plant. It does not display any of the genes characteristic of chloroplast DNA of the gymnosperm Pinus thunbergii (chlB, chlL, chlN, psaM, and ycf12). The majority of phylogenetic analyses of protein-coding genes of this chloroplast DNA suggests that Amborella is not the basal angiosperm and not even the most basal among dicots.