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We present the draft genomes of four strains of Rhizobium isolated from root nodules of Cojoba arborea, Lonchocarpus felipei, Mimosa pigra and Calliandra haematocephala in Costa Rica. Through comparative genomics including the estimation of the Average Nucleotide Identity (ANI), digital DNA-DNA hybridization (dDDH) and phylogenomic analysis we determined that Rhizobium sp. LEGMi-135b represents a potentially novel species near Rhizobium hainanense (ANI: 94%, dDDH=53.2%). The strain LEGMi-12c was associated with R. hainanense (ANI: 98%, dDDH=87%), strain LEGMi-166a to Rhizobium altiplani (ANI: 100%, dDDH=99.3%) and strain LEGMi-198b was related to R. cerradonense (ANI: 98%, dDDH=81.4%). Using functional annotation tools, we also determined in silico the presence of genes related to nodulation and nitrogen fixation such as fix, nif, nod, nol, and ntr in each strain. With this work, we provide valuable genomic resources of the genus Rhizobium that will be useful for future studies on rhizobial taxonomy, symbiosis, and ecology in tropical ecosystems.