In Mexico we have identified new species of bacteria of the genus Rhizobium and Sinorhizobium (now officially called Ensifer) such as S. mexicanum, S. chiapanecum, S. americanum, R. grahamii, R. mesoamericanum, and R. endophyticum, as well as new rhizobia lineages. Analysis based on genomic data shows that genetically related Rhizobium species significantly share their chromosomal genome but differ in genes contained in plasmids, except in some symbiotic plasmids that can be found even in unrelated species that contain the same simbiovar. Advances in rhizobia genomics have allowed us to propose new species using global genomic comparisons and this knowledge will contribute to the most appropriate use of these bacteria as biofertilizers.