The molecular responses to various abiotic stresses were investigated by the approaches with transcriptomic analysis based on an ACP system. Here we identified differentially expressed genes under abiotic stresses in alfalfa seedlings and they were mostly unknown genes and a few common stress-related genes. Among them, mitochondrial small HSP23 was responded by the diverse stress treatment such as heat, salt, As stresses and thus it could be a strong candidate that may confer the abiotic stress tolerance to plants. When expressed in bacteria, recombinant MsHSP23 conferred tolerance to salinity and arsenic stress. Furthermore, MsHSP23 was cloned in a plant expressing vector and transformed into tobacco, a eukaryotic model organism. The transgenic plants exhibited enhanced tolerance to salinity and arsenic stress under ex vitro conditions. In comparison to wild type plants, the transgenic plants exhibited significantly lower electrolyte leakage. Moreover, the transgenic plants had superior germination rates when placed on medium containing arsenic. Taken together, these overexpression results imply that MsHSP23 plays an important role in salinity and arsenic stress tolerance in transgenic tobacco. The results of the present study show that overexpression of alfalfa mitochondrial MsHSP23 in both eukaryotic and prokaryotic model systems confers enhanced tolerance to salt and arsenic stress. This indicates that MsHSP23 could be used potentially for the development of stress tolerant transgenic crops, such as forages.