The lysogenic phage CTXΦ of Vibrio cholerae can carry and transfer the cholera toxin gene ctxAB from toxigenic strains to non-toxigenic strains. CTXΦ also has a precursor, pre-CTXΦ，which does not carry ctxAB gene. In this study, we sequenced the genomes of four nontoxigenic serogroups O1 and O139 strains carrying pre-CTXΦ with the next generation sequencing. Both short-reading and long-reading sequencing were conducted to facilitate the assembly of long repeats. pre-CTXΦ prophage sequences were extracted from the genomes of these strains. The genes of CTXΦ receptor TcpA and the receptor-binding protein pIII in CTXΦ genome was subjected to sequence alignment, phylogenic tree construction and possible domains for protein-protein interactions. The tandem repeats of the different pre-CTXΦ alleles and their novel arrangement in the genomes were identified, and the precursor genome of classical type CTXΦ was also found. The arrangements of the pre-CTXΦ alleles in these strains were significantly different from the pandemic O1 El Tor strains. New sequences of the TcpA and the pIII were found in some strains. TcpA-pIII sequence correspondence analysis indicated the complicated interactions of the different sequence types of both proteins during the infection of pre-CTXΦ alleles. In addition, we have discovered a new type of pre-CTXΦ on small chromosome of VC702. The rstR-4 gene in VC702 has been disrupted by an insertion of a transposon which was firstly found in Klebsiella pneumoniae. Our study revealed new sequence types and arrangement of the pre-CTXΦ alleles and new evidence for better understanding the horizontal transfer of CTXΦ/pre-CTXΦ among the strains.