Variable number tandem repeats (VNTRs) are present in the control region of mitochondrial DNA (mtDNA) of the alligatorid species; however, the evolutionary dynamics of the repetitive sequences and the significance of the VNTRs in the context of genetic monitoring of these species are not well explored. The Chinese alligator, Alligator sinensis is critically endangered and is now largely in captive breeding. Previous studies in mitochondrial genes revealed little genetic diversity existing within the populations. We reported here the structural variation and evolutionary features of mtVNTRs in the Changxing population of the species. The mtVNTRs contained 676∼785 base pairs, made up by 5 distinct motifs repeated 31∼36 times in 32 individuals examined. The motifs were 21∼22 nts in length, with high sequence similarity between each other and with those of the American alligator (Alligator mississippiensis), indicating origination of the mtVNTRs from a single ancestral duplication unit in both species. The 5′ and 3′ portions of the repetitive sequences in the Chinese alligator were very much conserved among the individuals, while those in the middle showed a higher degree of sequence variation. The frequency of each motif appearing in the mtVNTRs showed positive correlation to the binding energy of the potential secondary structure the motif could adopt. 17 VNTR types, of which, 6 from the second generation and 12 from the third generation were identified from the samples. Analysis of the multiple VNTR types showed a high level of stochastic mutation within each generation. The suitability of the mtVNTRs as a marker to monitor the genetic differentiation of the Chinese alligator was also discussed.