Rabies in dogs continues to be a serious public health threat in many regions worldwide. Viet Nam is one of endemic countries of the disease and many fatal cases in dogs and human have been frequently reported over years. This study aimed to determine the seroprevalence and factors associated with the seroprevalence of captured dogs in slaughterhouses in Can Tho and Ben Tre provinces, the two epidemiologically representative locations of rabies in the Mekong delta (MD), Viet Nam. During 2020–2021, a total of 470 canine serum samples were collected from slaughterhouses in six districts for each of Ben Tre and Can Tho provinces and these collected sera were tested for detection of anti-rabies antibodies using indirect enzyme-linked immunosorbent assay (ELISA). Seroprevalence of rabies virus in Ben Tre was 5.94% (17 positive samples out of 286 collected samples) which was lower than the seroprevalence in Can Tho at 14.13% (26/184), respectively. Similarly, the mean value of antibody titer against rabies virus of captured dogs in Ben Tre (1.19±0.45IU/mL) was lower than that of in Can Tho (5.98±4.84IU/mL). Effects of several demographic factors such as breed, region and sex were not found for canine rabies seroprevalence. This study provides important information about seroprevalence of rabies for dogs in the MD and highlights necessity for vaccination program and surveillance for control and prevention of rabies in the area.