Although understanding non-random insertion of NUMT and carrying out certain function after insertion, helps with revealing the structure and determining the complete function of the genome, especially human genome, NUMTs have been used as experimental tools and have been beneficial in different biological fields even before having any knowledge about the function of NUMTs. For instance, NUMTs can be used not only as genetic markers but also as a tool for understanding the relative rate of mutation in the nucleus and the mitochondria as well as recreating evolutionary trees. The continuing process of NUMT integration into the nuclear genome is evidenced by the finding of NUMTs that have been inserted into the human genome after the human–chimpanzee divergence. Some of these NUMTs are variable with respect to the genomic presence or absence, indicating that they have only arisen recently in the human population, permitting them to be used as genetic markers of lineage. Using a protocol based on genome alignment to estimate the number of NUMT in closely related species, Hazkani-Covo and Graur could not only identify evolutionary events that may have affected NUMT composition in each genome but could also reconstruct the NUMT makeup in the common ancestor of human and chimpanzee. NUMTs can be also used to compare the rate of nonfunctional nuclear sequence evolution to that of functional mtDNA and determine the rate of evolution by the rate of mutation accumulation along NUMT sequences over time. The least selectively constrained regions are the segments with the most divergence from the mitochondrial sequence. One of the most promising applications of NUMT study is its use in the study of nuclear mutation. In metazoans, NUMTs are considered non-functional. Therefore, nuclear mutations can be distinguished from mitochondrial changes and the study of nucleotide substitution, insertion, and deletion would be possible. Additionally, the homology of paralogous NUMT sequences with the mtDNA allows testing for local sequence effects on mutation. All these information obtained from the study of NUMT fragments could be used to understand mitochondrial evolution as well as evolutionary processes throughout the history.