The study was conducted to analyze the genotypic and allelic frequencies of Myxovirus (Mx)-resistance gene in Philippine native chickens. DNA was extracted from blood and 101 bp of the Mx gene exon 13 was amplified and digested using PCR-RFLP. Digested products were visualized through polyacrylamide gel electrophoresis to determine the genotype of each chicken. Genotyping results showed that Philippine native chickens had higher frequencies of the favorable AA genotype and A allele than GG genotype and G allele, respectively. Similarly, commercial layer, but not broiler chickens, had higher frequencies of AA genotype and A allele. Moreover, the present study confirms the association of Mx genotype with genetic group, plumage color, and geographical location. Frequencies were not significantly different between sexes. Patani, Joloanon, and Labuyo genetic groups, black plumage color and native chickens from Mindanao were associated with AA genotype. Commercial broiler was more likely to be associated with GG genotype than AA and AG genotype.