Objective To preliminarily explore the infection status and molecular typing of Borrelia burgdorferi in rodents in parts of Fujian province. Methods Rodents were captured by the cage method in 5 counties (cities), i.e., Shaowu, Gutian, Shishi, Minhou, and Changle from April 2017 to June 2018. Nucleic acids were then extracted from rodent tissue samples (e.g., liver and kidney). After that, the fragments of 5S-23S rRNA were amplified by nested PCR, and sequencing results were analyzed by MEGA 6.0 software. Results A total of 192 rodents were captured, of which 81 were commensal rodents, accounting for 42.19% (81/192), and 111 wild rodents, accounting for 57.81% (111/192). Among all the rodents, four were detected to be positive for Lyme, accounting for 2.08% (4/192). Of the Lyme-positive rodents, one was commensal rodent, accounting for 1.23% (1/81) of all the commensal ones, and three wild rodents, accounting for 2.70% (3/111). Bioinformatics analysis revealed that SW14 from Shaowu and SS53 from Shishi were both B. valaisiana. The gene sequences of the two strains were identical or highly similar to those of B. valaisiana isolate R48 (EU160458.2) and B. valaisiana isolate 11 (JX888445.1), respectively. The gene sequences of both the SW15 from Shaowu and the GT38 from Gutian were different from those of above-mentioned B. valaisiana. Conclusion Rodents carry B. burgdorferi in the five surveyed counties (cities). The genotype (i.e., B. valaisiana) is consistent with that in the surrounding provinces.