The current epidemic of highly pathogenic avian influenza H5N1 virus is considered to pose a significant threat to the health of wild and domestic avian species, and even to human beings. The Black Sea-Mediterranean Flyway is one of the most important epidemic areas of H5N1. However, the epidemic along this flyway has not been fully explored. To better understand the role of hosts in the spread and evolution of H5N1 virus along the flyway, a phylogeographic study was conducted using haemagglutinin (HA) gene sequences obtained during 2005-2013. To infer phylodynamic spread in time and space, we used a flexible Bayesian statistical framework and modelled viral spatial diffusion as a continuous-time Markov-chain process along time-measured genealogies. Our results revealed that H5N1 virus isolated from wild birds showed an increase in genetic variation of HA gene from 2005-2007. The mean genetic distance of viruses isolated from poultry reached its peak in 2010, and dropped in 2011, increasing again in 2012-2013. The reconstruction of virus circulation revealed a different viral-migration network of H5N1 virus by different hosts. Western Russia constituted a link in viral migration from Russia to Europe and Africa. Cross-species transmission of H5N1 viruses predominated in the migration network of the Black Sea-Mediterranean Flyway. This might be due to the migration of birds across long distances and interaction between local poultry and migratory birds. Additionally, the short-distance spread of H5N1 viruses among poultry followed local transportation networks. Such findings will aid in developing effective disease control and prevention strategies.