Photosynthesis is the hallmark of plant evolution; the vast majority of plants are autotrophic and rely entirely on this process to fix carbon. As a consequence, the plastid genome (or plastome) is highly conserved across land plants with respect to its size, synteny, and gene content. Owing to this predictable structure as well as the low rates of nucleotide substitution, the plastome is a useful source of data for addressing phylogenetic questions. I use a rare structural change to the plastome as a phylogenetic marker to address the position of Gnetales within seed plants which has been difficult to resolve. The loss of all eleven plastid ndh genes support a 'gnepine' hypothesis or the placement of Gnetales as sister to Pinaceae. About 1% of flowering plants have lost all or some of their photosynthetic ability. These so-called heterotrophic plants are capable of obtaining water and/or nutrients from a host and are divided into two distinct groups: haustorial parasites, and mycoheterotrophs. In extreme cases, fully heterotrophic plants have completely lost the ability to photosynthesize. The phylogenetic position of heterotrophic plants has been difficult to resolve due to extensive changes to plastome size, structure, and content. Broad-scale angiosperm phylogenies indicate that the haustorial parasitism has evolved at least 11 times independently and there are at least 10 independent origins of mycoheterotrophy among land plants. Using a Southern hybridization approach combined with an extensive taxon sampling, I investigated the evolution of plastome protein coding gene content in parasitic Cuscuta (Convolvulaceae) and mycoheterotrophic Ericaceae. Common patterns include the early loss of the plastid ndh genes and extreme reduction in coding content of achlorophyllous species. A most intriguing result is the apparent loss of all plastid genes, including the highly conserved ribosomal RNA genes in Cuscuta section Subulatae ('O' clade), this condition that has only been inferred among the highly specialized parasites in Rafflesiaceae. Informed by these broad surveys, I further investigated the evolution of mycoheterotrophy in Ericaceae, using a select sampling across the trophic spectrum and a next generation sequencing approach. The plastomes of all Ericaceae species are highly rearranged and lack synteny with a typical plastome. Furthermore, positive selection was found to be acting on the rps, rpl, rpo, and ndh genes in a number of photosynthetic lineages. The plastid ndh genes are variable for their presence and absence in the partially mycoheterotrophic Pyroleae. The plastomes of fully mycoheterotrophic species are highly reduced with Allotropa virgata possessing the smallest plastome among land plants observed to date. Additionally, these plastomes have been reduced to encoding a highly divergent accD open reading frame, matK, and housekeeping genes that are generally under purifying selection. However, several ribosomal proteins and matK, were found to be under positive selection.