HIV-1 provirus is flanked by one long terminal repeat (LTR) at each terminal. The 5' LTR plays important roles in HIV-1 life cycle, especially, it determines HIV-1 transcription. However, there are 810 5' LTR entries exist in the HIV-1 sequence database, accounting for only 0.085% (810/949,484). In this study, we collected plasma samples from HIV-1-infected patients in Shenzhen province and got 219 5' LTR sequences. In addition, we found recombination in the LTR region. The recombinants (LS13145, LS11614, LS14862, and LS14863) possess an insertion of CRF01_AE segment at HXB2 482-630 bp (149 bp) in the skeleton of 5' LTR of subtype C. At the same time, our study found that the occurrence of recombination caused changes in many transcription factor binding sites. As the increasing investigation on 5' LTRs diversity and characterization, we will get a deeper understanding of HIV-1 transmission, evolution, and the basic mechanism of transcriptional regulation.