Symbioses are natural biotechnological systems in which soil bacteria, named rhizobia, form interactions with legumes, resulting in nitrogen fixation. Rhizobium leguminosarum bv. trifolii TA1 (RtTA1) genome is partitioned into chromosome and four megaplasmids. The macrorestriction map of RtTA1 genome was constructed and over 100 genetic markers on chromosome and plasmids were localized. In the RtTA1 genome, five large regions and many separate potential polysaccharide biosynthesis genes were found. All regions showed high degree of sequence identity and conserved synteny between R. leguminosarum bv. viciae (Rlv) and Rhizobium etli (Rhe). Comparative analyses of genetic maps of close relatives RtTA1, Rlv and Rhe showed significant chromosome colinearity, providing a basis for comprehensive analysis of R. leguminosarum genome evolution.