The covid-19 pandemic that occurred in the beginning of 2020 has affected all sectors, particularly in health and economic sectors. The Avian Influenza Virus (AIV), a zoonotic virus that have been reported endemic in Indonesia since 2003, might be affected by this condition. There is very limited information related AIV distribution and circulation due to covid-19 pandemic in Indonesia. This study aims to investigate the endemicity of the AIVs in Indonesia by conducting surveillance in several districts/cities in Central Java, West Java, Yogyakarta, and East Java Provinces during 2021. The samples were tested using the RT-PCR method and then DNA sequencing was carried out at Hemagglutinin and Matrix genes. The results of this study were obtained from 597 pool and individual samples from cloacal swabs, tracheal swabs, organs, and environmental swabs of poultry obtained from live poultry markets and poultry farms. The result revealed that 105 samples were tested positive for Influenza A (Matrix). Furthermore, AIV subtype-specific reverse transcription polymerase chain reaction (RT-PCR) from 105 samples tested positive for Influenza A showed that 4 samples tested positive for subtype H5 (3.8%), 4 samples tested positive for subtype H9 (3.8%), 8 samples tested positive for subtype H3 (7.6%), and no samples was found positive for subtype H10. The results showed that the AIV subtype H5N1 still circulating in Indonesia, interestingly the H3 subtype was found to be the predominant virus in this study. Influenza virus subtype H3 has a very diverse host range from birds to various mammalian species including pigs, horses, and dogs, and causes sporadic outbreaks in marine mammals. After the emergence of the A/Hong Kong/1968 (H3N2) pandemic virus, it became endemic and caused annual seasonal epidemics in humans. In China, Influenza virus subtype H3 has had a lineage in domestic poultry and has several subtypes that are H3N2, H3N3, H3N6, and H3N8, which have been isolated from domestic poultry globally. The infection of Influenza virus H3 Subtype can cause mild to severe disease. Experimental studies have also shown that the H3N8 subtype virus originating from poultry can replicate in the respiratory tract of mice, indicating that H3 isolates pose a threat of zoonotic infection. Therefore, the monitoring of H3 subtype AIVs and other AIVs subtype raised great concerns related to the potential threat to animal and human health and poses a potential risk to public health.