Vaccination can be a useful tool for control of avian influenza outbreaks in poultry, but its use is reconsidered in most of the countries worldwide because of its negative effects on the disease control. One of the most important negative effects is the potential for emergence of vaccine-resistant viruses. Actually, in the vaccination program in China and Mexico, several vaccine-resistant strains were confirmed. Vaccine-resistant strains usually cause a loss of the protection effectiveness of vaccination. Therefore, a vaccination program that engenders the emergence of the resistant strain might promote the spread of the resistant strain and undermine the control of the infectious disease, even if the vaccination protects against the transmission of a vaccine-sensitive strain. We designed and analyzed a deterministic patch-structured model in heterogeneous areas (with or without vaccination) illustrating transmission of vaccine-sensitive and vaccine-resistant strains during a vaccination program. We found that the vaccination program can eradicate the vaccine-sensitive strain but lead to a prevalence of vaccine-resistant strain. Further, interestingly, the replacement of viral strain could occur in another area without vaccination through a migration of non-infectious individuals due to an illegal trade of poultry. It is also a novel result that only a complete eradication of both strains in vaccination area can achieve the complete eradication in another areas. Thus we can obtain deeper understanding of an effect of vaccination for better development of vaccination strategies to control avian influenza spread.