Soybean is the world-leading legume crop. It fixes atmospheric nitrogen through symbiotic rhizobia bacteria that inhabit root nodules. It is predicted that large areas of the world will experience extensive drought conditions over the next few decades. Already Western Canada has been experiencing frequent and severe droughts over the last few decades. Therefore, evaluation of symbiotic nitrogen fixation in soybeans under drought stress is important to identify resistant varieties and use them in future breeding programs. We believe that there is a genetic variant(s) for nitrogen fixation under drought stress in short-season soybean varieties. The main objective of this study is to identify allelic variation associated with nitrogen fixation under drought stress in a short-season soybean varieties. A diversity panel of 140 early-maturity Canadian soybean varieties for which genome-wide genotypic data are available was used in this study. A greenhouse pot experiment was conducted to determine plant phenotypic traits and nitrogen fixation under drought stress. Seedlings were inoculated with Bradyrhizobium japonicum and the initial moisture content of the potting media was maintained at 80% field capacity. The drought treatment was imposed after three weeks of plant growth, where half of the plants were maintained at 30% field capacity and the rest at 80% field capacity until maturity. Five weeks after the growth, leaf chlorophyll content was measured using a SPAD meter. Leaf photosynthesis, stomatal conductance, and transpiration were measured using a portable LI-COR photosynthesis system. The initial results show genotypic variability for leaf chlorophyll content, where nitrogen accumulated in leaves under drought stress. Yield, yield parameters, and % nitrogen derived from atmosphere (%NDFA) will be measured at seed maturity. A genome-wide association study will be performed to identify allelic variation associated with nitrogen fixation under drought stress and provide molecular markers that will be useful in future breeding programs.