The double-stranded, circular mitochondrial DNA (mtDNA), which is present in all eukaryotic life forms, was initially discovered and characterized in the last century and has been widely used in evolutionary studies. Since then, a large number of studies have taken advantage of the genetic information encoded in this genome. Because of its small size in animals (in general), the technical ease of manipulating mitochondrial genome and the dynamics of its evolutionary change, this genome has been the workhorse of evolutionary studies over the past three decades. However, the ease with which nuclear DNA can be manipulated due to next generation sequencing (NGS) methods, has recently caused an expected dip in the use of mtDNA in evolutionary studies. This review examines the future of mitochondrial DNA as a useful tool in studies centered around evolution.