Goat’s milk benefits humans by providing nutrients like protein, calcium, fats, carbohydrates, vitamins, and minerals. In the holy Quran, Goat’s milk is mentioned 5 times indicating its importance to humans and nature. Due to the study of mislabelling of dairy products globally, the authenticity and traceability of commercialised milk are often questioned among the public. In the case of goat milk products, clear and accurate labelling is recommended with respect to the geographical origin of the products and the substances used in the products. This is to make sure that the correct decisions can be made by consumers. To investigate the phylogenetic relationship in this analysis, DNA sequence data and mitochondrial nucleotide sequences of raw (self-milking) and commercialised goat milk (Capra aegagrus hircus) from each state of Malaysia were used. For the reconstruction of the phylogenetic tree, Neighbour-Joining (NJ), Maximum Parsimony (MP) and Molecular Evolution were used. Following the manufacturer's (Promega, USA) protocol description, genomic DNA was isolated using the Wizard® Genomic DNA Purification Kit. By using Clustal X, multiple sequence alignment was performed. In addition, qualitative methodology of content analysis is also carried out. The congruent findings of the trees for Capra aegagrus hircus indicate that the commercialised samples of goat's milk are considered to be authentic based on the phylogenetic tree of our study. To our knowledge, there is still no recent study on the validity of goat milk in Malaysia, and this understanding will play an important role in educating customers about the authenticity of goods. Interestingly, Islamic perspectives are also studied for the benefits of society especially Muslims, hence increasing the development of integration of Naqli and Aqli knowledge.