A polymerase chain reaction (PCR) to detect a region of the A1 cholera toxin gene was applied to the identification of 43 Vibrio choleraestrains isolated from the recent outbreak in Argentina. A good correlation was observed between the GM1‐enzyme‐linked immunosorbent assay (GM1‐ELISA) to detect the B subunit of the enterotoxin and PCR. However, a V. choleraenon‐01 strain that was negative by the ELISA test, was positive by the PCR assay for the Al region. A second PCR test to detect the A2‐B coding region was developed to solve this case. We propose that routine detection of toxigenic V. choleraeby PCR should include analysis of A2‐B coding region or the whole cholera toxin operon.