Foods of animal origin in particular draw due attention with respect to authenticity of source. Although quality assurance system ensures correct labeling, documentation, and traceability, it requires cross checking as well. Hence, identification of species and sex of animal products is of paramount importance in the modern animal products trade. Buffalo meat is a high nutritive quality meat with huge export value from Asia. Adulteration of buffalo meat with beef is one of the problems faced especially in India wherein export of beef is completely prohibited. Array of techniques have been developed for species identification of buffalo meat; of which, molecular techniques which are highly specific and can be used for any tissue from the animal are used routinely in forensic laboratories in the last two decades. Some of the molecular techniques used for species identification of meat are Forensically Important Nucleotide Sequencing (FINS), species specific Polymerase Chain Reaction (PCR), PCR—Restriction Fragment Length Polymorphism, DNA micro array, etc. In this chapter, different molecular techniques reported for species authentication of buffalo meat are covered.