Influenza A viruses (IAVs) evolve via point mutations and reassortment of viral gene segments. The patterns of reassortment in different host species differ considerably. We investigated the genetic diversity of IAVs in wild ducks and compared it with the viral diversity in gulls. The complete genomes of 38 IAVs of H1N1, H1N2, H3N1, H3N2, H3N6, H3N8, H4N6, H5N3, H6N2, H11N6 and H11N9 subtypes isolated from wild mallard duck and gull habitants of a pond in Moscow city, Russia were sequenced. The sequences were closely related to those of avian IAVs isolated in Sweden and the Netherlands. The analysis of phylogenetic trees showed that stable viral genotypes do not persist from year to year in ducks owing to frequent gene reassortment. For comparison, similar analyses were carried out using sequences of IAVs isolated in the same period from ducks and gulls in the Netherlands. Our results revealed a significant difference in diversity and rates of reassorment of IAVs in ducks and gulls.