Genetic analysis of group A rotavirus recovered from fecal samples of children admitted to hospitals in Novosibirsk and Omsk during four epidemic seasons 2007, 2007/2008, 2009/2010, 2010/2011 was performed. A total of 1416 rotavirus isolates were genotyped using multiplex PCR. The isolates of the most common rotavirus genotypes G1P[8], G4P[8], G2P[4], G3P[8] co-circulated in Western Siberia during 2007-2011. In isolated cases G9P[8], G2P[8], G3P[9], and G4P[6] genotypes were detected. Change of dominant genotype from G1P[8] to G4P[8] occurred in 2008 in Omsk and in Novosibirsk in 2009 as well. Incidence and distribution of rotavirus genotypes differed and changed every epidemic season in both cities. The phylogenetic analysis based on VP4 (VP8*), VP7, and VP6 gene sequences showed that the majority of isolates from Novosibirsk and Omsk were clustered together and demonstrated high level homology with rotavirus isolates found in other regions of Eurasia. In addition, a rare P[8]b (OP354-like) subtype of the VP4 gene was identified in fourteen isolates (G9, G1, and G4) in Novosibirsk and in a single isolate Omsk08-381/G9P[8]b in Omsk. The results obtained in this study demonstrate the necessity of long-term monitoring of rotavirus isolates in Western Siberia. This is important for selection of rotavirus vaccine for immunization of infants, improvement of diagnostic kits and understanding of the epidemiology and the evolution of group A rotaviruses.