Molecular baraminology is a subdiscipline within the science of baraminology. Baraminology in general deals with how to classify organisms into different kinds, or baramins. Molecular baraminology uses a sequence similarity cutoff value to either join two species into the same baramin or separate them into two different baramins. Many mitochondrial and chloroplast genome baraminology studies have been performed, but a specific cutoff value has not been determined. To define this cutoff value, one can measure the range of sequence similarity values among species within the same kind across a large dataset. In this study, the mitochondrial genomes of 1,005 mammalian species were compared to one another and stored in an online database. For any kind, the lowest sequence similarity value was taken as a possible cutoff value. The distribution of all such minimum sequence similarity values was analyzed over various kinds at the taxonomic level of the genus, family, or order. For all three taxonomic levels the distribution of minimum sequence similarity values was normal, without showing multimodality. The correlation between the minimum sequence similarity and the number of genera/species in the family or the genus was weakly negative. The correlation between the minimum sequence similarity and the number of species in the order was strong and negative. Since the level of the kind rarely reaches that of the order, only genera and families were examined in more detail. The lowest minimum sequence similarity values for genera and families were 83.2% and 75%, respectively. Since the level of the kind for the mammal species used in the database was between the genus and the family, the sequence similarity cutoff value whereby two species can be classified into either the same or different baramins is within the range of 75–83.2%. Also, the distribution of mtDNA sequence similarity values for several hybrid mammals was analyzed to help determine the sequence similarity cutoff value. Hybridization is a strong indication that two species belong to the same kind. The minimum sequence similarity found in this analysis was 86.6%. Furthermore, a cumulative proportion function curve was plotted to depict the proportion of mtDNA sequence similarity values over series of sequence similarity values. Two inflection points between the values of 75–85% indicate that this might be the cutoff range that determines whether two species belong to the same or different kinds.Lastly, an online app called the Mitogenome Database was developed that allows users to perform their own mitochondrial DNA-based baraminology studies.