Background: The purpose of this study was to identify the genetic patterns of Streptococcus mutans by DNA finger printing among caries-active, caries-free, and in children with black tooth stains. Materials and Methods: In this in vitro study Ten children with black tooth stains and ten caries-free and caries-active children between 3 and 6 years of age were recruited. Saliva samples were collected using a sterile tube, followed by microbial culture of S. mutans, DNA isolation, and polymerase chain reaction amplification. The molecular weights of each band were converted into binary data, and data were entered into SPSS to generate similarity dendrograms. Results: Dendrogram interpretation of black tooth stain and caries-free samples revealed an identical genetic pattern in 15 samples with high genetic similarity. Dendrogram interpretation of black tooth stain and caries-active samples exhibited a greater genetic diversity. Conclusion: This study concludes that identical genotypes and high genetic similarity among isolates of the caries-free and black tooth stains. Polymorphism and genetic diversity exist between the black tooth stain and caries-active samples.