Trifolium pratense (red clover) and T. repens (white clover) inoculated with Rhizobium leguminosarum sv. trifolii strain U204 are used to improve pastures in Uruguay. Although inoculation is a common practice in the country, there has been a progressive abandonment by farmers because they do not always see the benefits. The presence of efficient rhizobial populations may be one of the reasons why a response to inoculation is not always observed. We studied the identities and phylogenetic relationships among the clover rhizobia populating Uruguayan soils by analysis of 16S rRNA genes, ITS sequences and housekeeping (atpD, glnII, recA, rpoB) and symbiotic (nodA, nodC, nifH) genes. Strains like P3 and P33, isolated from the endemic Trifolium polymorphum, are inefficient in red and white clover. These strains clustered separately from the symbionts of these clovers. Bacteria which are efficient in red and white clovers clustered in either of two groups: one, represented by isolate 249, are likely naturalized rhizobia derived from the inoculant U204; and other included strains like U317 and N2, which share symbiotic genes with the inoculant. We hypothesize that these strains may be derived from native strains that acquired symbiotic gene from inoculant strains. These types of rhizobia are strong candidates for a second generation of clover inoculants for Uruguay.