Borrelia burgdorferi sensu lato (s.l.) complex, the etiological factor of Lyme disease, includes over a dozen species of bacteria and 3 pathogenic within it. According to many authors, the clinical symptoms of borreliosis depend on the species that cause the disease. The most frequent symptom of early localized borreliosis is erythema migrans (EM). The aim of the research was to determine species of B. burgdorferi s.l. in 32 patients from the Western Pomerania region in whom EM has been recognized. Blood samples of patients were investigated by PCR-RFLP method, with the use of enzyme differentiating species. The DNA of spirochetes was detected in 25 patients (25/32, 78.1%), compared with 23/32 (71.8%) of ELISA positive patients. Among 25 positive samples, 10 contained the DNA of B. garinii (10/25, 40%), 5 the DNA of B. afzelii (5/25, 20%), 4 the DNA of B. burgdorferi sensu stricto (s.s.) (4/25, 16%) and in 6 samples (6/25, 24%) the DNA of both B. garinii and B. afzelii was found. The DNA of B. burgdorferi s.l. spirochetes may be detected in patients with EM after antibiotic treatment. The most frequent species in patients with EM from the Western Pomerania region is B. garinii. Infections with more than one species of B. burgdorferi s.l. may occur in patients with EM.