This study reports the whole‑genome sequence (WGS) of an endophytic bacterial strain isolated from efficient root nodules of Vigna unguiculata collected from Ksar Ben Aissa (Tmimoun, Algeria). The strain, identified as Ensifer sp., exhibits nitrogen‑fixing activity and associates with the host plant in a symbiotic manner, contributing to nitrogen nutrition in low‑fertility soils. Whole‑genome sequencing will provide valuable insights into the genetic basis of nodule‑associated endophytic behaviour and nitrogen fixation, facilitating the development and application of this strain in sustainable agriculture in desert environments.