The examination of internal plant structures referred to as anatomy study has long been employed for taxonomical purposes particularly in the case of the Zingiberaceae family. The scarcity of information about anatomical differences between limestone and non-limestone gingers as well as the relationship between anatomy and soil nutrients leads to these findings. This research specifically focuses on the anatomy study of Zingiberaceae originating from both limestone and non-limestone soils in Kelantan. Utilizing light microscopy and scanning electron microscopy, the study comprehensively reports on the anatomical features of leaves, pseudostems, rhizomes, and roots of selected wild gingers. Independent T-tests were employed to emphasize significant differences between wild gingers inhabiting the two types of soils. Notably, stomata length in limestone Globba leucantha at (0.85 ± 0.03) μm was found to be significantly greater compared to the non-limestone G. leucantha at (0.23 ± 0.01) μm. In pseudostems, significant differences in the length and width of vascular bundles were observed in Etlingera littoralis and Etlingera punicea. In limestone E. littoralis, the length of the vascular bundle is notably longer, measuring (0.40 ± 0.03) mm, compared to the non- limestone E. littoralis with a length of (0.29 ± 0.02) mm. Similarly, in rhizomes, significant differences in the length and width of vascular bundles were found in E. punicea and Zingiber spectabile. The length of vascular bundles in limestone E. punicea measures (0.31 ± 0.05) mm, contrasting with the non-limestone E. punicea, which has a shorter length of (0.18 ± 0.04) mm. In the root, significant differences in the length and width of vascular bundles were noted in E. punicea, G. leucantha and Z. spectabile. Soil samples were also collected and analyzed for nutrient content, revealing the presence of phosphorus, potassium, sulphur, calcium, magnesium, aluminium, manganese, iron, copper, zinc, boron, and sodium. Spearman Rho correlation analysis demonstrated a positive association between stomata length and the length of guard cells in leaves with the presence of phosphorus in the soil. This research contributes significantly to filling the knowledge gap regarding the impact of soil nutrients on plant anatomy in vegetative parts, shedding light on the intricate relationship between soil conditions and anatomical features in Zingiberaceae.