Fifty-four strains of H5N1 highly pathogenic avian influenza (HPAI) virus were isolated from wild birds in the ecosystems of northern Eurasia and from poultry in the south of western Siberia (July 2005), at the mouth of Volga River (November 2005), at Uvs-Nur Lake on the boundary of the Great Lakes Depression in western Mongolia and the Tyva Republic of Russia (June 2006), in the vicinity of Moscow (February 2007), in the southeastern part of the Russian Plain (September 2007 and December 2007), and in the far east (April 2008) of the Russian Federation and were phenotypically characterized and deposited into the Russian state collection of viruses. Complete genome nucleotide sequences for 24 strains were obtained and deposited into GenBank. In all cases when strains were isolated from both wild birds and poultry in the same outbreak these strains were genetically closely related to each other. Until 2008 all HPAI H5N1 strains isolated in northern Eurasia clustered genetically with the viruses from Kukunor Lake (Qinghai Province, China), known as genotype 2.2 or the “Qinghai-Siberian” genotype. The viruses from the Qinghai-Siberian genotype have continued to evolve from those initially introduced into western Siberia in 2005 into two genetic groups: “Iran–North Caucasian” and “Tyva-Siberian.” In vitro replication potential (50% tissue-culture infectious dose in porcine embryo kidney) of Qinghai-Siberian strains decreased over time, which could reflect decreasing virulence. Comparison of genome sequences with biological characteristics of the respective strains permitted us to identify point mutations in PB2, PB1, PA, HA, NP, NA, M2, NS1, and NS2 that possibly influenced the level of replication potential. The HPAI H5N1 virus, which penetrated into the south of the Russian Far East in spring 2008, belonged to genotype 2.3.2.