Injecting drug users (IDUs) are the major risk group for HIV-1 infection in the China-Myanmar borderarea. There are a large number of Burmese IDUs living in Yunnan (Yunnan-mIDUs) who might beassociated with the cross-border transmission of HIV-1. From 2010 to 2013, 617 Yunnan-mIDUs wererecruited from three counties of Yunnan, 19.0% of whom were detected to be HIV-1 positive byserologicaltesting.PartialHIV-1p17,pol,vif-env,andenvgeneswereamplifiedfromthepositivesamplesand were sequenced. Phylogenetic and HIV-1 subtyping analyses revealed that HIV-1 recombinantforms (RFs), including RF_BC (36.4%), RF_01BC (26.1%), RF_01C (9.1%) and RF_01B (1.1%), werepredominant among this cohort. Of the identified HIV-1 strains, 14.8%, 9.1% and 3.4% belonged tosubtype C, CRF01_AE and subtype B, respectively. Transmission cluster analysis showed that sequencesfrom the Yunnan-mIDUs formed transmission clusters not only with those from Burmese IDUs but alsowith those from Chinese IDUs, indicating that Yunnan-mIDUs might acquire HIV-1 infection from orspreadHIV-1toboth BurmeseandChineseIDUs. Phylogeographic analysesrevealedthreecross-bordertransmission patterns associated with Yunnan-mIDUs, in which Yunnan-mIDUs served as the crucialnodes linking the Burmese and Chinese IDUs. These results suggest that Yunnan-mIDUs are a potentialviralreservoirforthediffusionofHIV-1inYunnanandplayapivotalroleinthebidirectionalcross-bordertransmission of HIV-1 in the China-Myanmar border region. More intervention efforts that focus onYunnan-mIDUs are recommended in Yunnan’s campaign against HIV/AIDS.