Purpose: To describe the genotypes distribution of Orientia tsutsugamushi, in Guangzhou, and explore differences in clinical and laboratory features among genotypes. Method: We collected blood or eschar samples of all scrub typhus cases reported in 2013 from 10 district hospitals positive for PCR. We further tested the PCR-positive samples for DNA sequencing and phylogenetic analysis. We collected the demographic, clinical, and laboratory data by questionnaire and medical records. Result: A total of 589 samples were tested and 40 were PCR positive. Four genotypes were identified: Karp (52.2%), Kato (22.5%), Gilliam (12.5%), and TA763 (7.5%). Two new strains (ZCX90 and CHX5 strain) were previously unidentified in Guangzhou. Gilliam type cases were more likely to have continuous fever (60.0%). Only Kato genotype cases presented with splenomegaly. For laboratory features, Kato group had higher level of white blood cell count (16.44 x 10(12)/L) than normal range and other groups. Total bilirubin and direct bilirubin in Gilliam group (10.10 mu M and 3.05 mu M, respectively) were both lower than other groups and normal value. Conclusion: Continuous fever and splenomegaly may be the distinctive symptom of Gilliam and Kato genotype cases, respectively. Karp genotype remained dominant in Guangzhou, but attention should be paid to the emergence of new types or variation of existing genotypes.