The current phylogenetic classification of aPMV-1 strains is based on either full or partial nucleotide sequence of the M, F, or L genes. To determine if all genes in the viral genome provided consistent phylogenetic profiles, we obtained 54 full length class II aPMV-1 sequences from Genbank and generated nucleotide data sets for each of the six genes and a concatenated sequence of all protein coding regions. Maximum likelihood (ML) phylogenies were reconstructed for all sequence data sets under the appropriate nucleotide substitution model selected for each data set ( Figure 1 ). Each gene tree and the concatenated tree revealed seven distinct genotypes within the class II aPMV-1. However, genotype affiliations were not congruent among different genes ( Figure 1A ). While genotype III, IV, V, VI, and VII were monophyletic, genotype I and II showed inconsistent phylogenetic relationships ( Figure 1A and B). Three distinct patterns of affiliations of genotype I and II were observed among different gene trees. The NP, HN, L, and concatenated gene trees consistently placed genotypes I and II in a sister clade to other genotypes. In the P gene tree, genotype II formed a basal clade while genotype I clustered with the remaining genotypes and in the M and F gene trees, genotype I was the basal clade and genotype II clustered with the remaining genotypes.