The first HIV-1 recombinant between CRF0I_A.E and subtype C, NP1809, has been identified in Thailand. The nearly full genome was polymerase chain reaction amplified, sequenced and phylogenetically analysed. NP1809 was a complex recombinant, with at least 15 breakpoints. Gag and gp120 were subtype C, whereas pol and intracellular gp41 were CRF01_AE. We report a new inter-subtype recombinant of CRF01_AE and subtype C, establishing for the first time the presence of subtype C genetic material in Thailand.