We have determined draft whole genome sequences for B. burgdorferi isolates N40 and JD1 and the plasmids from isolate 297. The comparison of these draft sequences sheds considerable light on a number of aspects of their biology including horizontal exchange of genetic information, plasmid diversity, lipoprotein variability, and plasmid partitioning. We find that plasmids cp9, cp26, the cp32s, and lp54 are quite constant in gene organization among the four strains, but the remaining linear plasmids are quite variable in organization. We analyze the replication, partitioning, and compatibility gene cluster on the plasmids from these four strains and propose to use them in a universal B. burgdorferi plasmid nomenclature system.