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Chilli (Capsicum annuum) is an important spice crop in Bangladesh. This crop is very sensitive to waterlogging. Floating agriculture is an innovative system led by the local people of the southern region of Bangladesh, in which seedlings of vegetables are produced in low-lying areas using different aquatic macrophytes. An experiment was carried out to evaluate the viability of chilli cultivation in waterlogged areas, based on physiological and biochemical responses using floating agriculture. Eight different chilli varieties were subjected to floating agriculture in two different agronomic seasons. A soil-based chilli cultivation system was also trialled, to compare the utility of this method. To evaluate the performance of chilli in floating beds, plant water status, photosynthetic parameters, and leaf tissue concentrations of Na+, K+, NO3− and PO43−, chlorophyll, ascorbic acid and proline were assessed. This study shows that macrophytes utilised in floating beds provide favourable conditions for chilli cultivation under waterlogged conditions. Among the different varieties, Sakata 653 in summer and Jhilik in winter responded better than others. As the performance of chilli in the floating agriculture system was satisfactory in comparison with soil-based cultivation, floating agriculture can be an alternative agronomic method for chilli cultivation in waterlogged areas of Bangladesh. Floating agriculture is a promising way of crop cultivation under submergence. Production of chilli (Capsicum annuum), an important spice crop, is greatly affected by waterlogging. In submerged conditions, floating agriculture serves an alternative agronomic means of chilli cultivation. [ABSTRACT FROM AUTHOR]