Avian influenza viruses (AIVs) pose a continuous threat to global poultry production and animal health, maintained largely within wild bird reservoirs and dispersed along migratory flyways. Among these, the low-pathogenic H6N1 subtype circulates widely across East Asia and is a key subject of genomic surveillance. In this study, we characterized the hemagglutinin (HA) and neuraminidase (NA) gene segments of seven H6N1 viruses isolated from 9,206 wild bird fecal samples across 10 key breeding habitats in Mongolia (April–October, 2022–2024) and evaluated their genetic relationships with seven H6N1 strains isolated from fecal samples of wild birds (n?=?7,419) and domestic ducks (n?=?79,386) in the Republic of Korea (ROK) between September 2023 and April 2024 using Bayesian phylogenetic analyses. All analyzed isolates belonged to the Northeast Asian lineage, primarily diverging into two regional subclades around 2016–2017 (time to the most recent common ancestor [tMRCA]: HA, Dec 2017; NA, Nov 2016). Both HA and NA phylogenies exhibited a ladder-like topology structured across distinct geographical regions, indicating localized variant generation and turnover. Comparable evolutionary rates and restricted reassortment between HA and NA segments underscore strong co-adaptation driven by functional balance between HA receptor binding and NA enzymatic activity. Despite the substantial geographical distance between Mongolia and the ROK, these H6N1 isolates demonstrated close genetic connectivity within the Northeast Asian lineage (Bayes factor?>?100). Their surface gene diversification was primarily shaped by antigenic drift alongside restricted regional intra- and inter-clade reassortment. Given the continuous evolutionary dynamics of surface glycoproteins, sustained transboundary monitoring across wild waterfowl and poultry populations is warranted to track regional H6N1 variants.