Objective To investigate the occurrence and the characteristics of human immunodeficiency virus (HIV)-1 co/super-infection among high-risk populations in Myanmar.Methods Forty-six HIV-1 positive plasma in Myanmar were collected. Possible cases with HIV-1 co/super infection were identified by discordant sequence results obtained with different polymerase chain reaction (PCR)/sequencing primers or by ambiguous readings in direct sequencing. HIV-1 quasispecies in plasma were then characterized by clonal sequence analysis of independent PCR-clones generated by TA cloning method. Thereafter, their phylogeny and recombinant structure were investigated. Results Co/super infection was identified in 3 (6.5 %) cases among the 46 screened HIV-1 positive patients.All of these three patients were heterosexuals and were co/super infected with CRF01_AE/subtype B′recombinants. Conclusions HIV-1 co/super infections are relatively common and provide a prerequisite for rapid generation of new recombinant forms in Myanmar.