We report here a novel HIV-1 intra-CRF01_AE recombinant form (CRF01-1AE/CRF01-6AE) composed of CRF01_AE transmission clusters 1 and 6, identified among heterosexuals in Fujian, with one breakpoint observed in vif gene. The CRF01_AE region I (HXB2: 868-5184) of the recombinant was clustered with the CRF01_AE transmission cluster 1, which is mainly circulating among IDUs and heterosexuals from the southern and southwestern China, with the support of 100% bootstrap value. The CRF01_AE region II (HXB2: 5185-9605) of the recombinant was clustered with the CRF01_AE transmission cluster 6, which is mainly prevailing among heterosexuals from southern China, with the support of 100% bootstrap value. To our best knowledge, this is the first detection of a novel HIV-1 intra-CRF01_AE recombinant form (CRF01-1_AE/CRF01-6_AE) in Fujian Province, which indicates ongoing active HIV-1 transmission among heterosexuals in this region. It may help illustrate CRF01_AE genetic diversity and contribute to our understanding of HIV-1 epidemiology, pathogenesis, and vaccine development.