Global surveillance of influenza A/H5N1 is critical for improvement in disease management, and is especially important for early detection, rapid intervention, and a possible reduction of the impact of an influenza pandemic. There is a great demand for new technological methods for viral discovery. We described a semiconductor-base oligonucleotide microarray for influenza A virus identification and monitoring. Central to this approach was microarray designed to identify influenza A virus hemagglutinin subtypes 1 through 16 and neuraminidase subtypes 1 through 9. To further characterize this influenza A virus, we proposed Bioedit program for accurately identifying viral sequences by discovering sequence signature, which was enough distinctive information for the sequence identification. The 8 H5N1-RNA samples were collected and extracted from birds and mammal samples between 2003 to 2006, which were used to analyze H5N1 genotypic testing with semiconductor-base oligonucleotide microarray. One hundred percent (8/8) of the samples tested were subtyped correctly as H5N1. After absolutely correct subtyping from microarray signal intensity result, the method used microarray output combined with Bioinformatic tool for identification and monitoring of genetic variations of H5N1. The outstanding feature of this assay is its capability to distinguish different strains of H5N1. Ninety percent HA (4/5) and ninety percent NA (4/5) genes were sequenced correctly in accordance with previous examinations performed by classical diagnostic methods. This assay was a convenient and practical tool for the study of avian influenza viruses, providing important HA and NA data more rapidly than conventional methods. However, the protocol monitoring of the new strain H5N1 is recommended for further study.