There are a number of underexplored plant species from the family of Rutaceae despite their economic importance, including Glycosmis perakensis V.Naray. Therefore, the main purpose of this study is to enhance its taxonomic characterization and identification of this plant species by examining the morphology and anatomy of selected parts. The histological procedure for G. perakensis stems and leaves were optimized by increasing the incubation time for the fixation, clearing, and infiltration steps of the standard paraffin embedding method. Different types of stains were also used to identify and differentiate the plant tissues. The anatomy of plant parts such as stem, leaf, and petiole were studied using light microscopy. Pellucid dots and stomata exist on both abaxial and adaxial leaf surfaces. Statistical analysis on stomatal index and stomatal density showed a significant difference between abaxial and adaxial surfaces. Histological analyses showed the presence of sclerenchyma, collenchyma, and parenchyma cells, vascular bundle, prismatic crystals of calcium oxalate, and secretory cavities in the plant leaf and stem transverse sections. This is the first study reporting on the histological morphology of stem, petiole, and leaf of G. perakensis. The findings of this study will be a valuable tool for the identification of this plant.