Honey is a bee product known for its nutritive and therapeutic properties and has been used since ancient times. These properties of honey are associated with its physical and chemical composition. The composition of honey includes carbohydrates, proteins, water, vitamins, minerals, and phenolic compounds. It also contains several specific compounds that can be used as markers of its botanical origins. Phenolic compounds have been identified as the secondary metabolites in honey, and they are crucial for identifying honey based on its botanical and geographic origins. These compounds, such as flavonoids and phenolic acids, are natural antioxidants that significantly contribute to the bioactive and therapeutic properties of honey. These compounds not only serve as natural antioxidants but also act as floral markers for identifying and authenticating honey. Furthermore, phenolic compounds in honey are recognized for their substantial antioxidant capacity and various beneficial pharmacological properties, including wound healing, anti-inflammatory effects, and anti-tumor effects. This chapter aims to assess the effective role of phenolic compounds for determining the botanical origin of honey by examining the literature studies.