Plants need the right and appropriate combination of nutrients to live, grow and reproduce. Soil fertility depends on the availability of all essential macro and micronutrients and uptake by the crops grown on it. Genetically modified crop varieties have various advantages over traditional crop varieties. Area under cultivation of such genetically modified crop is increasing worldwide including India. In India genetically modified BT Cotton is grown since 2002. Maharashtra is an important state for cotton cultivation and production. It is contended by researchers that continued cultivation of genetically modified BT cotton crop may create harm to the soil fertility and availability of nutrient. Present study deal with the comparison of Zinc micronutrient and potential of hydrogen ion (pH) concentration of soil, on which BT Cotton and non BT Cotton cultivated soils of farmers belonging to Nandurbar, Dhule and Jalgoan District of North Maharashtra. Standard procedures were followed for collection of soil samples, quantitative analysis of zinc and pH of the soils.