Cocirculation of subtype B and CRF01-AE in Southeast Asia has led to the establishment of new recombinant forms. In our previous study, we found five samples suspected of being recombinants between subtype B and CRF01-AE, and here, we analyzed near full-length sequences of two samples and compared them to known CRFs-01B, subtype B, and CRF01-AE. Five overlapped segments were amplified with nested PCR from PBMC DNA, sequenced, and analyzed for genome mosaicism. The two Indonesian samples, 07IDJKT189 and 07IDJKT194, showed genome-mosaic patterns similar to CRF33-01B references from Malaysia, with one short segment in the 3′ end of the p31 integrase-coding region, which was rather more similar to subtype B than CRF01-AE, consisting of unclassified sequences. These results suggest gene-specific continuous diversification and spread of the CRF33-01B genomes in Southeast Asia.