Lyme borreliosis in North America is caused by B. burgdorferi which is vectored by the black-legged tick Ixodes scapularis. The transmission cycle of B. burgdorferi in the northeastern USA is believed to be driven mainly by white-footed mouse, Peromyscus leucopus, a highly abundant and reservoir competent. However, many other terrestrial mammals and birds are commonly infected by this spirochete. Recently, for Europe, it was discovered that the various genospecies that cause Lyme borreliosis (and some subtypes) are host associated. Therefore, this study was designed to answer the question whether distinct genotypes within B. burgdorferi are amplified by different mammalian host species. Mammals were captured in a woodland area at Lake Gaillard, Connecticut, in summer 2002 and 2003. Engorged tick larvae recovered from six host species were allowed to molt to the next developmental stage, and newly-molted nymphal ticks were tested for spirochete infection by RT-PCR, followed by direct nucleotide sequencing of the intergenic spacer region between the 16S and 23S rDNA genes. The data show that mammalian host species other than mice substantially contribute to the circulation of B. burgdorferi. However, different host species maintain distinct sets of genotypes with the highest diversity in mice, whereas squirrels and chipmunks seem to support only a few genotypes. Furthermore, the transmissibility of the genotypes from infected hosts to ticks varied amongst the host species. We conclude that the fitness of any one genotype is relative to host species.