Low molecular weight biogenic amines (BAs) have been reported in fermented foods such as histamine, tyramine, tryptamine, putrescine, cadaverine, and phenylethylamine, which are generated by decarboxylation of histidine, tyrosine, tryptophan, ornithine, lysine, and phenylalanine. Normal concentration of BAs causes normal metabolic functions in plants and animals. Excessive consumption of BAs causes health issues such as blood pressure and headache. BAs have been identified by polymerase chain reactions followed by high-performance liquid chromatography. These techniques are costly and time consuming when sample size is large. In recent era, in silico analysis is acknowledgeable for identification of specific genes for large sample size. In this chapter, rapid annotation subsystem technology protocol is explained to identify BA coding genes.