Mitochondria and mitochondrial DNA are known to be highly motile. Molecular analysis revealed that several proteins are bound between mitochondrial DNA and mitochondrial inner membrane. However, nucleoid formed by these proteins is involved in the replication and duplication of mitochondrial DNA and it remains unclear whether mitochondrial DNA keeps binding the mitochondrial inner membrane or not. When nucleoid is necessary during cell cycle, it would be formed probably. When nucleoid is formed in the manner dependent on mitochondrial DNA sequence, the changes in the sequence would result in the equilibrium shifted to dissociation. This implies that the important information on changes in mtDNA accompanied with various symptoms is obtained by quantitative analysis of mtDNA dynamics. In this review, theoretical background of two typical methods, i.e., particle trajectory and image correlation spectroscopy, and several results of the pilot experiment are introduced.