The millions of deaths from cholera during the past 200 y, coupled with the morbidity and mortality of cholera in Haiti since October 2010, are grim reminders that
Vibrio cholerae
, the etiologic agent of cholera, remains a scourge. We report the isolation of both
V
.
cholerae
O1 and non-O1/O139 early in the Haiti cholera epidemic from samples collected from victims in 18 towns across eight Arrondissements of Haiti. The results showed two distinct populations of
V. cholerae
coexisted in Haiti early in the epidemic. As non-O1/O139
V
.
cholerae
was the sole pathogen isolated from 21% of the clinical specimens, its role in this epidemic, either alone or in concert with
V
.
cholerae
O1, cannot be dismissed. A genomic approach was used to examine similarities and differences among the Haitian
V
.
cholerae
O1 and
V
.
cholerae
non-O1/O139 strains. A total of 47
V
.
cholerae
O1 and 29
V
.
cholerae
non-O1/O139 isolates from patients and the environment were sequenced. Comparative genome analyses of the 76 genomes and eight reference strains of
V
.
cholerae
isolated in concurrent epidemics outside Haiti and 27
V
.
cholerae
genomes available in the public database demonstrated substantial diversity of
V. cholerae
and ongoing flux within its genome.