Avian metapneumovirus (aMPV) is a respiratory pathogen and includes four subtypes, which are differentially distributed worldwide. In Israel, two aMPV subtypes, A and B, are cocirculating in an area with a relatively high density of poultry houses. We performed a longitudinal survey in commercial flocks of turkeys and chickens (six and two flocks, respectively) with differing vaccination programs. This study revealed that all monitored flocks were infected by aMPV during the sampling period, as detected either by serology or by molecular methods. Moreover, to identify the subtypes infecting the birds and to distinguish between field and vaccine strains, we sequenced fragments of the attachment glycoprotein gene. This analysis revealed that both vaccine and field strains of both aMPV-A and -B could be recovered from the birds. In four out of six turkey flocks, aMPV field strains were recovered, emphasizing the broad distribution of this highly contagious pathogen. Importantly, in two out of four vaccinated turkey flocks, homologous field subtypes of aMPV-A or -B were detected even after boost administration, suggesting failure of the vaccine to protect the flocks from secondary infection. Overall, the results of this longitudinal study call for a more efficient vaccination program against aMPV, which is critical for an area of intensive commercial poultry farming.