Cholera, caused by Vibrio cholerae O1 and O139, has high incidences in regions with neglected populations, especially in terms of sanitation. V. cholerae can be transported by ship ballast water which makes it a D2 standard evaluation bioindicator for the International Convention for the Control and Management of Ship´s Ballast Water and Sediments. The objective of this is to identify the presence of the organism in the port area of the City of Rio de Janeiro (Brazil), in samples of surface water and ballast tanks, contributing to the analysis of the ballasting process and its interactivity with human health. In superficial and vessel sampling campaigns, the non-toxic form of the organism was detected. The conclusive facts suggest the vulnerability of the area, methodological elaboration for the selection of ships to be sampled, incentives for installation, inspection of the D2 standard and constant monitoring of port waters and vessels, aiming to prevent possible cholera outbreaks caused by the ballast of the modal maritime in region.