Plastid genomes in the flowering plant family Geraniaceae are known to be highly rearranged based on complete sequences representing the four major genera Erodium, Geranium, Monsonia, and Pelargonium. In this paper we report on the genome sequence of a second species of Erodium, E. carvifolium, representing the second major clade (clade II) in the phylogeny of this genus. Comparison of this genome sequence to the previously published sequence of E. texanum from clade I demonstrates that the plastid genomes of these two species encode the same number of proteins but differ greatly in their relative degree of rearrangement; 14 kb of additional sequence in E. texanum contains complex repeats associated with rearrangement endpoints, whereas the plastid genome of E. carvifolium is streamlined at 116 kb and displays no unique alterations in gene order. Furthermore, these species from both major clades of Erodium contain intact NADH dehydrogenase (ndh) genes, but the 11 ndh genes are represented as pseudogenes in a small clade of 13 species. It is unclear whether plastid-encoded ndh genes have been lost entirely or functionally transferred to the nucleus. This is the third report of the absence of functional ndh genes, and the current study describes the most recent loss of these genes among photosynthetic seed plants and the second such loss among angiosperms. The other ndh losses from Pinaceae/Gnetales and Orchidaceae are much more ancient. Comparative biochemistry between Erodium species with and without plastid-encoded ndh genes may elucidate changes in photosynthetic function and the role of the Ndh complex.