Mitochondria are subcellular organelles in which oxidative phosphorylation and other important biochemical functions take place within the cell. Within these organelles is a genome, called the mitochondrial (mt) genome, which is distinct from, but cooperates closely with the nuclear genome of the cell. Investigating mt genomes has significant implications for various fundamental research areas, including mt biochemistry and physiology, and, importantly, such genomes provide a rich source of markers for population genetic and systematic studies. While approximately 250 complete mt genome sequences have been determined for a range of metazoan organisms from various phyla, few of these represent parasitic helminths. Until 1998, only two mt genome sequences had been determined for parasitic nematodes, in spite of their socio-economic importance and the need for investigations into their population genetics, taxonomy and evolution. However, since that time, there has been some progress. The main focus of the present chapter is to review the state of knowledge of the mt genomics for parasitic nematodes, to describe recent technological improvements to mt genome sequencing, to summarize applications of mt gene markers for studying the systematics and population genetics of parasitic nematodes, and to emphasize prospects and opportunities for future research in these areas.