Potato virus Y (PVY) is the type member of genus Potyvirus and one of the most common species and most pernicious of Potyvirus. PVY has a wide host range and infects several important solanaceous crops, including potato, tomato and tobacco. In Vietnam, potato virus Y is a severe disease in almost all tobacco growing areas. The disease had a high incidence and caused severe damage especially in Bac Son, Lang Son Province, in 2015. The objective of this study was to determine the genetic diversity of PVY infecting tobacco in the major growing tobacco region of Northern Vietnam which is essential for disease prevention. In this study, tobacco leaves with typical symptoms of PVY were collected from major growing tobacco fields in three provinces in Northern Vietnam, including Cao Bang, Lang Son and Bac Giang. CP gene fragments encoding the capsid protein of PVY were amplified by Reverse Transcript PCR and sequenced by ABI 3500 system. The sequences obtained were analyzed and classification trees were built by using MEGA6 software. From the results, we classified four groups of PVY, including PVY⁰, PVY^c, PVY^NTN and a new group that is similar to group KC296833 on potato in China but we did not determine the strain of the new PVY. PVY⁰ is the most common group and PVY isolated in Lang Son is the most diverse. Two strains PVY^c, PVY^NTN were only found in tobacco cultivation in Lang Son Province, and the four strains were found in Bac Son. The determination of genetic diversity is important in the tobacco growing areas in Northern Vietnam and is essential for PVY control in the field.