While the previous phylogenetic analyses of AIV H9N2 in Israel had mainly focused on phylogenetics and on describing different virus introductions into the country, for the first time, the H9N2-HA gene evolutionary history has been examined taking into account its origin, evolution and phylodynamics. The present study reveals the Israeli H9N2 molecular evolution rate, the virus molecular clock and skyline plot. The molecular skyline plot showed two major increments in population diversity sizes, the first which had occurred in 2003, the second between the end of 2007 and the first half of 2008. Between 2004 and 2007 the population size had proved to be constant. The two peaks correspond to the appearance of the 3rd and 4th major genetic groups, as well as to the introduction of two H9N2 vaccines. The mean evolution rate was 6.123 E-3 substitutions/site/year, typical of avian influenza viruses. The time interval from the most recent common ancestor was 12.3 years, corresponding to the year 2000, when H9N2 was first isolated in Israel.