This is the author accepted manuscript. The final version is available from Taylor and Francis (Routledge) via the DOI in this record.Cotton (Gossypium sp.) is a major crop grown under rainfed conditions in Vertisols and associated soils in semi-arid tropical (SAT) regions of Peninsular India. In recent years, cotton productivity has declined due to various biophysical factors including pest and diseases, seasonal water stress soil degradation and poor crop management practices. In this study, we compare two methods for evaluating the suitability of Vertisols for cotton in contrasting two agro-ecological regions viz., sub-humid moist (SHM) region and semi-arid dry(SAD) were characterized. Twelve cotton growing Vertisols (seven from SHM and five from SAD) were evaluated for their suitability for cotton cultivation using soil quality index (SQI) and modified Sys-FAO method. SQIs were calculated using the weighted additive index from transformed scores of selected indicators by principal component analysis. For Sys-FAO method both biophysical and soil characteristics were considered for suitability evaluation. We found that the soils of SHM region were moderately suitable for cotton cultivation with soil moisture as the major limiting factor, whereas the soils of SAD region are marginally suitable due to high exchangeable sodium percentage and poor hydraulic conductivity. From this, it may be concluded that the weighted SQI has better agreement with the cotton yield.