Chrysomya megacephala larvae can easily be identified using cheap traditional microscopy techniques. Nevertheless, identification using taxonomy keys may be hampered, if the morphological characteristics of the larvae are incomplete, or immature for microscopic identification. To overcome the difficulty of species determination, molecular identification has gained relevance and is applied in forensic investigations. This study aimed to identify a novel target gene, known as the gustatory receptor 1 gene (CmegGr1), which has never been used for identification. The third instar larvae of Ch. megacephala (n = 30) and eight other forensically important fly species were obtained from two sources; rabbit carcasses and the Forensic Entomology Unit collection. Their DNAs were extracted and the CmegGr1 gene was amplified using polymerase chain reaction (PCR). The resulting sequences were subjected to phylogenetic analysis. A 209 bp fragment of the CmegGr1 gene was successfully amplified in 80% (24/30) of Ch. megacephala samples, while all of the non-Ch. megacephala species were not amplified. The phylogenetic analysis revealed that the evolutionary tree of CmegGr1 shares many traits with the 21a gustatory receptors of Calliphora stygia and Lucilia cuprina (Gr21a), which are also classified as necrophagous fly species. The high specificity of species identification was demonstrated in the present study using DNA barcoding, which led to the conclusion that the CmegGr1 gene could serve as an alternative marker for identifying Ch. megacephala.