We analyzed 30 V. cholerae O1 biotype El Tor isolates from the Central African Republic (CAR) by whole-genome sequencing. Fourteen of these isolates — collected between 1997 and 2011 — were sequenced in a previous study. The 24 V. cholerae O1 biotype El Tor isolates sequenced here consisted of the remaining 16 isolates from CAR — including all the 2016 isolates — and 10 isolates from neighboring countries (Chad and the Democratic Republic of the Congo)