Drought is one of the major environmental factors limiting biomass and seed yield production in agriculture. In this research we focused on plants from Fabaceae family, which have a unique ability for establishment of symbiosis with nitrogen-fixing bacteria, and are relatively susceptible to water limitation. We present the changes in nitrogenase activity and global gene expression occurring in Medicago truncatula and Lotus japonicus root nodules during water deficit. Our results prove a decrease in the efficiency of nitrogen fixation as well as extensive changes in plant and bacterial transcriptomes shortly after watering cessation. We show for the first time that not only symbiotic plant component, but also Sinorhizobium meliloti and Mesorhizobium loti bacteria residing in the root nodules of M. truncatula and L. japonicus, respectively, adjust their gene expression in response to water shortage. Although our results demonstrate that both M. truncatula and L. japonicus root nodules are susceptible to water deprivation, they indicate significant differences in plant and bacterial response to drought between tested species, which may be related to various type of root nodules formed by these species. Overall design: RNA was obtained from Medicago truncatula and Lotus japonicus non-inoculated roots (R) and root nodules either subjected to drought for two (T2) or four (T4) days, or well-watered control (T0). Two biological replicates for each sample was obtained. Each biological replicate consisted of roots or nodules harvested from 10-12 plants. RNA obtained from root nodules contained both plant and bacterial RNA. For Medicago truncatula the compatible rhizobium species is Sinorhizobium meliloti, for Lotus japonicus - Mesorhizobium loti.