In this study, we report the presence of the El Tor CTXΦ and classical CTXΦ inVibrio choleraeO1 strains isolated from Varanasi, India. Polymerase chain reaction, DNA sequencing and restriction fragment length polymorphism revealed that, although ctx-positive strains isolated after 1990 contain CTXΦ harbouring El Tor type ofrstRand classicalctxB, strains isolated before 1990 contain El Tor type ofrstRand El TorctxB. TwoV. choleraeO1 strains (VC104 and VC106) represent an altered/hybrid strain containing the RS1 element followed by CTXΦ prophage harbouring El Tor typerstRand classicalctxBon the chromosome-I and RS2 element followed by second copy of CTXΦ prophage harbouring classical typerstRand classicalctxBon the chromosome-II. This is the first report of occurrence of El Tor CTXΦ harbouring classicalctxBand classical CTXΦ harbouring classicalctxBin chromosome-I and -II, respectively in diarrhoeal isolates ofV. choleraeO1 El Tor strains from Varanasi, India, and that had been isolated in 1992.