Abstract: Objective To understand the transmission of scrub typhus in Menghai county, Yunnan province. Methods Blood samples were collected from clinical diagnosed and suspected scrub typhus cases at acute and convalescence phases in Menghai from June to September in 2011. Nested polymerase chain reaction (nPCR) was conducted to detect the groEL gene of Orientia tsutsugamushi (Ot) in blood clots from patients at acute phase. Indirect immunofluorescence assays (IFA) were conducted to detect IgG antibodies against Ot in sera from patients. Results A total of 36 blood clot samples were tested with PCR, and 25 samples were positive woth Ot nucleic acid. The groEL gene fragments of 14 positive samples were cloned and then sequenced. According to the homology and phylogenetic analysis; the 14 strains shared 99%-100% homology of nucleotide and 100% homology of amino acid. They were very close to and shared high homology with the strains BJ-TZ-OT-O39, AH-GD-OT-S6, UT213, Kato and SH205 from GenBank. Of 17 patients detected at both acute phase and convalescence phase, 11 had a 4-fold increase in their Ot-IgG titer by IFA. Overall, 26 cases were diagnosed with scrub typhus (15 molecular biological confirmations and 11 serological confirmations). Conclusion The serological and molecular biological detections confirmed the transmission of scrub typhus in Menghai. Molecular epidemiological analysis showed that the circulating strains of Ot in Menghai was with stable genetic characteristics and obvious regional characteristics.