Construction and comparison of phylogenetic trees, the standard approach to determining the host-specific lineage of influenza A virus genes is tedious and expensive. In this study, panels of monoclonal antibodies (Mabs) produced against the matrix proteins (M1) of A/WSN and A/PR/8/34 and the nucleoprotein (NP) of A/WSN were assessed for their value in identifying the hosts of origin of the M1 and NP genes in influenza virus isolates and in mapping the proteins' functional domains. Using ELISA against a broad spectrum of reference viruses, we found two Mabs against the NP (150/4 and 469/6) to be useful in determining host-specific lineage. Comparative sequence analysis placed five amino acids within the antigenic domains recognized by Mab 150/4 and two amino acids within the domains recognized by 469/6. One Mab against the NP (5/1) recognized a conserved epitope that is present on each of the 36 influenza A viruses tested. This epitope may be a type-specific determinant for influenza A viruses and an RNA binding site. Monoclonal antibodies to M1 did not discriminate among species, but they did contribute information to the construction of a functional map of M1. These results demonstrate that Mabs to defined protein epitopes can provide useful information on the molecular epidemiology of influenza viruses.