The Orthomyxoviridae is a family of single strained RNA viruses including five genera: Influenza virus A, Influenza virus B, Influenza virus C, Thogotovirus, and Isavirus. Usually, Influenza viruses are identified by antigenic differences in their nucleoprotein and matrix protein. In this paper, we propose an algorithm to determine a set of suitable restriction enzymes for producing recognizable restriction maps on Orthomyxoviridae. Our method is applied to viral strains of highly pathogenic avian influenza (HPAI), containing potentially homozygous, heterozygous, and various genetic variations. In the analysis of CAPS (Cleaved Amplified Polymorphic Sequence) subtyping, our method outperforms the RNA coding of representative and epidemiologically significant human wild-type viruses, including H3N8, H5N1, H5N9, H7N1, H7N7, and H9N2. These isolates are analyzed by CAPS with enzymes AgeI, EciI, KpnI, and XbaI. The HPAI strains show a different RFLP (Restriction Fragment Length Polymorphism) profile by comparing with other low pathogenic avian influenza (LPAI) strains. We provide a rapid, specific, and reproducible identification of the genotypes on Orthomyxoviridae. It permits us to quickly confirm subtypes of Orthomyxoviridae.